UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-K
  þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 FOR THE FISCAL YEAR ENDED DECEMBER 31, 2008
 OR
 o
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 FOR THE TRANSITION PERIOD FROMTO.
 Commission file number: 001-32567
 ALON USA ENERGY, INC.
  Delaware
    
    74-2966572(State of incorporation)
    
    (I.R.S. Employer Identification No.)7616 LBJ Freeway, Suite 300, Dallas, Texas
    
    75251(Address of principal executive offices)
    
    (Zip Code)
   Title of each class
    
    Name of each exchange on which registeredCommon Stock, par value
$0.01 per share
    
    New York Stock Exchange
  o þ
 o þ
 þ o
 o
  Large accelerated filer o
    
    Accelerated filer þ
    
    Non-accelerated filer o
    
    Smaller reporting company o(Do not check if a smaller reporting company)
 o þ




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TABLE OF CONTENTS
   PagePART IITEMS 1. AND 2. BUSINESS AND PROPERTIES
    
    
    1ITEM 1A. RISK FACTORS
    
    
    27ITEM 1B. UNRESOLVED STAFF COMMENTS
    
    
    35ITEM 3. LEGAL PROCEEDINGS
    
    
    35ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS
    
    
    35PART IIITEM 5. MARKET FOR REGISTRANTS COMMON EQUITY, RELATED
STOCKHOLDER MATTERS AND ISSUER PURCHASE OF EQUITY
SECURITIES
    
    
    36ITEM 6. SELECTED FINANCIAL DATA
    
    
    38ITEM 7. MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL
CONDITION AND RESULTS OF OPERATIONS
    
    
    40ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT
MARKET RISK
    
    
    73ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA
    
    
    75ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON
ACCOUNTING AND FINANCIAL DISCLOSURE
    
    
    75ITEM 9A. CONTROLS AND PROCEDURES
    
    
    75ITEM 9B. OTHER INFORMATION
    
    
    75PART IIIITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT
    
    
    76ITEM 11. EXECUTIVE COMPENSATION
    
    
    76ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS
AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS
    
    
    76ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
    
    
    76ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES
    
    
    76PART IVITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
    
    
    77
  i




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PART I
 
 ITEMS 1. AND 2. BUSINESS AND PROPERTIES.
 Statements in this Annual Report on Form 10-K, including those in Items 1 and 2, Business and
Properties, and Item 3, Legal Proceedings, that are not historical in nature should be deemed
forward-looking statements that are inherently uncertain. See Forward-Looking Statements in
Managements Discussion and Analysis of Financial Condition and Results of Operations in Item 7
for a discussion of forward-looking statements and of factors that could cause actual outcomes and
results to differ materially from those projected.
 COMPANY OVERVIEW
  www.alonusa.com
  www.sec.gov www.alonusa.com www.alonusa.com
 
    
    Compensation Committee Charter;
    
    Audit Committee Charter;
    
    Corporate Governance Guidelines; and
    
    Code of Business Conduct and Ethics.
  1




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BUSINESS
   Refining and Unbranded Marketing
  Big Spring Refinery
       2




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##### 



Year Ended December 31,2008
    
    2007
    
    2006Bpd
    
    %
    
    Bpd
    
    %
    
    Bpd
    
    %Refinery throughput:Sour crude
    
    
    31,654
    
    
    
    83.8
    
    
    
    58,607
    
    
    
    86.0
    
    
    
    58,529
    
    
    
    89.4Sweet crude
    
    
    4,270
    
    
    
    11.3
    
    
    
    5,017
    
    
    
    7.4
    
    
    
    2,987
    
    
    
    4.6Blendstocks
    
    
    1,869
    
    
    
    4.9
    
    
    
    4,521
    
    
    
    6.6
    
    
    
    3,897
    
    
    
    6.0Total refinery throughput (1)
    
    
    37,793
    
    
    
    100.0
    
    
    
    68,145
    
    
    
    100.0
    
    
    
    65,413
    
    
    
    100.0Refinery production:Gasoline
    
    
    14,266
    
    
    
    38.4
    
    
    
    32,135
    
    
    
    47.5
    
    
    
    29,671
    
    
    
    46.0Diesel/jet
    
    
    10,439
    
    
    
    28.2
    
    
    
    19,676
    
    
    
    29.1
    
    
    
    20,651
    
    
    
    32.0Asphalt
    
    
    4,850
    
    
    
    13.1
    
    
    
    7,620
    
    
    
    11.3
    
    
    
    6,147
    
    
    
    9.5Petrochemicals
    
    
    1,221
    
    
    
    3.3
    
    
    
    3,980
    
    
    
    5.9
    
    
    
    4,465
    
    
    
    6.9Other
    
    
    6,298
    
    
    
    17.0
    
    
    
    4,190
    
    
    
    6.2
    
    
    
    3,627
    
    
    
    5.6Total refinery production (2)
    
    
    37,074
    
    
    
    100.0
    
    
    
    67,601
    
    
    
    100.0
    
    
    
    64,561
    
    
    
    100.0Refinery utilization (3)
    
    
    52.3
    %
    
    
    
    
    
    
    92.5
    %
    
    
    
    
    
    
    90.8
    %
 
 (1)
    
    Total refinery throughput represents the total of crude oil and blendstock inputs in the
refinery production process.(2)
    
    Total refinery production represents the bpd of various products produced from processing oil
and other refinery feedstocks through the crude unit and other conversion units at our Big
Spring refinery.(3)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds.  Big Spring Refinery Raw Material Supply
   3




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Crude Oil Pipelines
  Crude Oil Pipelines
    
    Status
    
    Miles
    
    ConnectionsAmdel
    
    Sunoco Throughput
    
    
    504
    
    
    Midland and NederlandWhite Oil
    
    Sunoco Throughput
    
    
    25
    
    
    Garden City (Amdel) and Big SpringMesa Interconnect
    
    Owned
    
    
    4
    
    
    Mesa pipeline and Big SpringCenturion
    
    Owned (leased to
Centurion)
    
    
    3
    
    
    Centurion pipeline and Big Spring
    Big Spring Refinery Production
 Gasoline
 Distillates
 Asphalt
 4




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Petrochemical Feedstocks and Other
 Big Spring Refinery Transportation Fuel Marketing
   Unbranded Transportation Fuel Marketing
 Jet Fuel Marketing
 Product Supply Sales
 Big Spring Product Pipelines
  5




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##### 



ExpirationProduct Pipelines
    
    Access
    
    Miles
    
    Connections
    
    DatePlains (1)
    
    Lease
    
    
    38
    
    
    Coahoma and Midland
    
    
    2012Fin-Tex
    
    HEP throughput
    
    
    137
    
    
    Midland and Orla (Holly)
    
    
    2020Holly
    
    Lease
    
    
    133
    
    
    Orla and El Paso
    
    
    2018Trust
    
    HEP throughput
    
    
    332
    
    
    Big Spring/Abilene/Wichita Falls
    
    
    2020Dyess JP-8
    
    HEP throughput
    
    
    2
    
    
    Abilene and Dyess Air Force Base
    
    
    2020River
    
    HEP throughput
    
    
    47
    
    
    Wichita Falls and Duncan (Magellan)
    
    
    2020Carswell
    
    Owned
    
    
    148
    
    
    Abilene and Fort Worth
    
    
    N/A
 
 (1)
    
    The description of the Plains pipeline does not include a 4-mile pipeline that we own
connecting Big Spring and Coahoma, Texas.      Product Terminals
  6




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WorkingTerminals
    
    Access
    
    Capacity (1)
    
    Supply Source
    
    Mode of DeliveryBig Spring, Texas (2)
    
    Owned
    
    
    331
    
    
    Pipeline/refinery
    
    Pipeline/truckAbilene, Texas
    
    HEP
    
    
    111
    
    
    Pipeline
    
    Pipeline/truckWichita Falls, Texas
    
    HEP
    
    
    189
    
    
    Pipeline
    
    TruckDuncan, Oklahoma
    
    Owned (3)
    
    
    154
    
    
    Pipeline
    
    PipelineOrla, Texas
    
    HEP
    
    
    116
    
    
    Pipeline
    
    PipelineSouthlake, Texas
    
    Terminalling
Agreement
    
    
    212
    
    
    Pipeline
    
    TruckTotal
    
    
    
    
    1,113
 
 (1)
    
    Measured in thousands of barrels.(2)
    
    Includes the tankage located at our Big Spring refinery.(3)
    
    The terminal is owned, but the underlying real property is leased.  California Refineries and Terminals
     7




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##### 



Year Ended December 31,
    
    Period Ended December 31, 2006 (1)2008
    
    2007Bpd
    
    %
    
    Bpd
    
    %
    
    Bpd
    
    %Refinery throughput:Sour crude
    
    
    8,014
    
    
    
    25.8
    
    
    
    20,839
    
    
    
    33.7
    
    
    
    37,171
    
    
    
    61.9Heavy crude
    
    
    22,590
    
    
    
    72.6
    
    
    
    40,700
    
    
    
    65.9
    
    
    
    22,533
    
    
    
    37.5Blendstocks
    
    
    495
    
    
    
    1.6
    
    
    
    223
    
    
    
    0.4
    
    
    
    362
    
    
    
    0.6Total refinery
throughput (2)
    
    
    31,099
    
    
    
    100.0
    
    
    
    61,762
    
    
    
    100.0
    
    
    
    60,066
    
    
    
    100.0Refinery production:Gasoline
    
    
    4,141
    
    
    
    13.7
    
    
    
    7,318
    
    
    
    12.1
    
    
    
    6,806
    
    
    
    11.6Diesel/jet
    
    
    7,481
    
    
    
    24.8
    
    
    
    13,360
    
    
    
    22.1
    
    
    
    11,026
    
    
    
    18.9Asphalt
    
    
    9,214
    
    
    
    30.5
    
    
    
    19,006
    
    
    
    31.5
    
    
    
    19,500
    
    
    
    33.3Light Unfinished
    
    
    0
    
    
    
    0.0
    
    
    
    3,071
    
    
    
    5.1
    
    
    
    6,144
    
    
    
    10.5Heavy Unfinished
    
    
    9,182
    
    
    
    30.4
    
    
    
    16,793
    
    
    
    27.9
    
    
    
    2,938
    
    
    
    5.0Other
    
    
    192
    
    
    
    0.6
    
    
    
    793
    
    
    
    1.3
    
    
    
    12,126
    
    
    
    20.7Total refinery
production (3)
    
    
    30,210
    
    
    
    100.0
    
    
    
    60,341
    
    
    
    100.0
    
    
    
    58,540
    
    
    
    100.0Refinery utilization (4)
    
    
    
    
    
    
    46.3
    %
    
    
    
    
    
    
    85.9
    %
    
    
    
    
    
    
    83.8
    %
 
 (1)
    
    2006 data includes our Paramount refinery for the period from August
1, 2006 through December 31, 2006 and our Long Beach refinery for the
period from September 28, 2006 through December 31, 2006.(2)
    
    Total refinery throughput represents the total of crude oil and
blendstock inputs in the refinery production process.(3)
    
    Total refinery production represents the bpd of various products
produced from processing crude oil and other refinery feedstocks
through the crude units and other conversion units at our California
refineries.(4)
    
    Refinery utilization represents average daily crude oil throughput
divided by crude oil capacity, excluding planned periods of downtime
for maintenance and turnarounds. Reflects the effects of downtime
associated with a planned turnaround of our No. 2 crude unit at the
Paramount refinery in March and April 2007 and the downtime to
optimize our refining and asphalt economics in 2008.  8




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California Refineries Raw Material Supply
  Crude Oil Pipelines
  Crude Oil Pipelines
    
    Status
    
    Miles
    
    ConnectionsParamount Crude
    
    Owned
    
    
    2.5
    
    
    Paramount and East Hynes TerminalChevron Crude
    
    Third Party
    
    
    15
    
    
    Paramount and local gathering systemNo. 3/No. 4
    
    Owned
    
    
    13
    
    
    Long Beach and Long Beach HarborBP
    
    Third Party
    
    
    1
    
    
    Long Beach and East Hynes Terminal
   California Refineries Production
 Gasoline
 Distillates
 9




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Asphalt
 Light and Heavy Unfinished Feedstocks
 California Refineries Transportation Fuel Marketing
    California Product Pipelines/Terminal
   Product Pipelines
    
    Access
    
    Miles
    
    ConnectionsLine 145
    
    Owned and Leased
    
    
    8
    
    
    Paramount to a connection with Line 145Line 166
    
    Leased
    
    
    2
    
    
    Connects to Line 145 to Carson City,
California (Kinder Morgan)
  California Feedstock Pipelines
  10




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Feedstock Pipelines
    
    Terminal
    
    Access
    
    Tankage (1)
    
    Miles
    
    ConnectionsChevron No.1
    
    
    
    Leased
    
    
    
    
    
    
    4
    
    
    Connects our
Paramount and Long
Beach refineries to
our Lakewood TerminalLakewood
    
    Owned
    
    
    110
    
    
    
    
    
    
    Connects the Chevron
No. 1 pipeline to our
Line 160 pipelineLine 160
    
    
    
    Owned
    
    
    
    
    
    
    7.1
    
    
    Connects the Lakewood
Terminal to our
leased tanks at
Kinder Morgan, other
refiners and third
party customersKinder Morgan
    
    Leased
    
    
    180
    
    
    
    
    
    
    Connects to our Black
Oil Pipeline for
deliveries to other
refiners and third
party customersLine 35, L-52, E-12A
    
    
    
    Owned
    
    
    
    
    
    
    4
    
    
    Connects our Long
Beach and Paramount
RefineriesBlack Oil Pipeline
    
    
    
    Owned
    
    
    
    
    
    
    19
    
    
    Connects the Kinder
Morgan Terminal and
Plains Pipeline
System to LA Basin
refiners and
waterborne terminals
 
 (1)
    
    Measured in thousands of barrels. Krotz Springs Refinery
        11




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Period Ended December 31, 2008 (1)Bpd
    
    %Refinery throughput:Light sweet crude
    
    
    43,361
    
    
    
    74.5Heavy sweet crude
    
    
    11,979
    
    
    
    20.6Blendstocks
    
    
    2,844
    
    
    
    4.9Total refinery throughput (2)
    
    
    58,184
    
    
    
    100.0Refinery production:Gasoline
    
    
    25,195
    
    
    
    42.8Diesel/jet
    
    
    26,982
    
    
    
    45.9Heavy oils
    
    
    1,402
    
    
    
    2.4Other
    
    
    5,258
    
    
    
    8.9Total refinery production (3)
    
    
    58,837
    
    
    
    100.0Refinery utilization (4)
    
    
    
    
    
    
    66.6
    %
 
 (1)
    
    2008 data includes our Krotz Springs refinery for the period from July 1, 2008 through
December 31, 2008.(2)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock
inputs in the refinery production process.(3)
    
    Total refinery production represents the barrels per day of various products produced from
processing oil and other refinery feedstocks through the crude unit and other conversion units
at our Krotz Springs refinery.(4)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds. Refinery
throughput and production for 2008 reflects the effects of shutdowns during hurricanes Gustav
and Ike and limited crude supply due to widespread electrical outages following the
hurricanes. Krotz Springs Refinery Raw Material Supply
     12




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Krotz Springs Refinery Production
 Gasoline
 Distillates
 Heavy Oils and Other
 Krotz Springs Refinery Transportation Fuel Marketing
   Krotz Springs Refinery Product Pipeline
   Asphalt
  13




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Texas Asphalt Marketing
  14




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West Coast Asphalt Marketing
    Asphalt StorageTerminals
    
    Capacity (1)
    
    Receipt Capabilities
    
    Delivery CapabilitiesCalifornia Refineries
    
    
    731
    
    
    Refinery, Rail, Truck
    
    Rail, TruckWillbridge, OR refinery
    
    
    1,129
    (2)
    
    Refinery, Rail, Truck, Marine
    
    Rail, Truck, MarineElk Grove, CA
    
    
    307
    
    
    Rail, Truck
    
    TruckBakersfield, CA
    
    
    183
    
    
    Rail, Truck
    
    TruckMojave, CA
    
    
    283
    
    
    Rail, Truck
    
    TruckRichmond Beach, WA
    
    
    702
    (2)
    
    Rail, Truck, Marine
    
    Truck, MarineFernley, NV (3)
    
    
    254
    
    
    Rail, Truck
    
    TruckPhoenix, AZ
    
    
    165
    
    
    Rail, Truck
    
    TruckFlagstaff, AZ
    
    
    25
    
    
    Rail, Truck
    
    TruckFredonia, AZ
    
    
    79
    
    
    Truck
    
    Truck
 
 (1)
    
    Measured in thousands of barrels.(2)
    
    Storage figures for Willbridge and Richmond Beach include tanks in service for storage of
crude oil, fuel oil or other products.(3)
    
    50% interest.  15




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Retail and Branded Marketing
  Retail
    Location
    
    Owned
    
    Leased
    
    TotalBig Spring, Texas
    
    
    6
    
    
    
    1
    
    
    
    7El Paso, Texas
    
    
    13
    
    
    
    74
    
    
    
    87Lubbock, Texas
    
    
    17
    
    
    
    5
    
    
    
    22Midland, Texas
    
    
    9
    
    
    
    9
    
    
    
    18Odessa, Texas
    
    
    10
    
    
    
    25
    
    
    
    35Wichita Falls, Texas
    
    
    8
    
    
    
    4
    
    
    
    12Abilene, Texas
    
    
    33
    
    
    
    8
    
    
    
    41Waco, Texas
    
    
    11
    
    
    
    3
    
    
    
    14Albuquerque, New Mexico
    
    
    12
    
    
    
    11
    
    
    
    23Other
    
    
    29
    
    
    
    18
    
    
    
    47Total stores
    
    
    148
    
    
    
    158
    
    
    
    306
   16




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##### 



Convenience Store Management and Employees
 Distribution and Supply
 7-Eleven License Agreement
 Technology and Store Automation
 Branded Marketing
   Distribution Network and Distributor Arrangements.
 17




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##### 



FINA Brand Sub-Licensing.
 FINA Minimum Standards Program.
 Payment Card Processing.
 Technology.
 Competition
   18




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##### 



19




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##### 



Government Regulation and Legislation
 Environmental Controls and Expenditures
  Environmental Expenditures
    20




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##### 



21




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##### 



Remediation Efforts
     22




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##### 



Environmental Indemnity from FINA
 Environmental Insurance
 Environmental Indemnity to HEP
  23




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##### 



Environmental Indemnity to Sunoco
 Other Government Regulation
     Employees
  24




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##### 



Properties
  Executive Officers of the Registrant
  Name
    
    Age
    
    PositionDavid Wiessman
    
    
    54
    
    
    Executive Chairman of the Board of DirectorsJeff D. Morris
    
    
    57
    
    
    Director, President and Chief Executive OfficerShai Even
    
    
    40
    
    
    Senior Vice President and Chief Financial OfficerJoseph Israel
    
    
    37
    
    
    Chief Operating OfficerClaire A. Hart
    
    
    53
    
    
    Senior Vice PresidentJoseph A. Concienne
    
    
    58
    
    
    Senior Vice President of RefiningAlan Moret
    
    
    54
    
    
    Senior Vice President of SupplyHarlin R. Dean
    
    
    42
    
    
    Senior Vice President  Legal, General Counsel and SecretaryMichael Oster
    
    
    37
    
    
    Senior Vice President of Mergers and AcquisitionsJimmy C. Crosby
    
    
    49
    
    
    Vice President of Refining  California RefineriesDavid Foster
    
    
    51
    
    
    Vice President of Refining  Big SpringWilliam Wuensche
    
    
    48
    
    
    Vice President of Refining  Krotz SpringsWilliam L. Thorpe
    
    
    62
    
    
    Vice President of Asphalt OperationsKyle McKeen*
    
    
    45
    
    
    President and Chief Executive Officer of Alon BrandsJoseph Lipman*
    
    
    63
    
    
    President and Chief Executive Officer of SCS
  David Wiessman
 Jeff D. Morris
 Shai Even
 25




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##### 



Joseph Israel
 Claire A. Hart
 Joseph A. Concienne
 Alan Moret
 Harlin R. Dean
 Michael Oster
 Jimmy C. Crosby
 David Foster
 26




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##### 



William Wuensche
 William L. Thorpe
 Kyle McKeen
 Joseph Lipman
 
 ITEM 1A. RISK FACTORS.
  The price volatility of crude oil, other feedstocks, refined products and fuel and utility services
may have a material adverse effect on our earnings, profitability and cash flows.
  
    
    changes in global and local economic conditions;
    
    domestic and foreign demand for fuel products;
 27




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##### 




    
    worldwide political conditions, particularly in significant oil producing regions such
as the Middle East, West Africa and Venezuela;
    
    the level of foreign and domestic production of crude oil and refined products and the
level of crude oil, feedstock and refined products imported into the United States;
    
    utilization rates of U.S. refineries;
    
    development and marketing of alternative and competing fuels;
    
    commodities speculation;
    
    federal and state government regulations; and
    
    local factors, including market conditions, weather conditions and the level of
operations of other refineries and pipelines in our markets.
    Our profitability depends, in part, on the sweet/sour crude oil price spread. A decrease in this
spread could negatively affect our profitability.
  The profitability of our California refineries depends, in part, on the light/heavy crude oil price
spread. A decrease in this spread could negatively affect our profitability.
  The dangers inherent in our operations could cause disruptions and could expose us to potentially
significant losses, costs or liabilities.
  28




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##### 



We are subject to interruptions of supply as a result of our reliance on pipelines for
transportation of crude oil and refined products.
  If the price of crude oil increases significantly, it could reduce our profit on our fixed-price
asphalt supply contracts.
  Our operating results are seasonal and generally lower in the first and fourth quarters of the
year.
  If the price of crude oil increases significantly, it could limit our ability to purchase enough
crude oil to operate our refineries at full capacity.
  Changes in our credit profile could affect our relationships with our suppliers, which could have a
material adverse effect on our liquidity and our ability to operate our refineries at full
capacity.
  29




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##### 



Competition in the refining and marketing industry is intense, and an increase in competition in
the markets in which we sell our products could adversely affect our earnings and profitability.
  Our indebtedness could adversely affect our financial condition or make us more vulnerable to
adverse economic conditions.
  
    
    we may be limited in our ability to obtain additional financing to fund our working capital
needs, capital expenditures and debt service requirements or our other operational needs;
    
    we may be limited in our ability to use operating cash flow in other areas of our business
because we must dedicate a substantial portion of these funds to make principal and interest
payments on our debt;
    
    we may be at a competitive disadvantage compared to competitors with less leverage since we
may be less capable of responding to adverse economic and industry conditions; and
    
    we may not have sufficient flexibility to react to adverse changes in the economy, our
business or the industries in which we operate.
  Competition in the asphalt industry is intense, and an increase in competition in the markets in
which we sell our asphalt products could adversely affect our earnings and profitability.
   30




---



##### 



Competition in the retail industry is intense, and an increase in competition in the markets in
which our retail businesses operate could adversely affect our earnings and profitability.
   We may incur significant costs to comply with new or changing environmental laws and regulations.
    We may incur significant costs and liabilities with respect to environmental lawsuits and
proceedings and any investigation and remediation of existing and future environmental conditions.
  31




---



##### 



We could incur substantial costs or disruptions in our business if we cannot obtain or maintain
necessary permits and authorizations or otherwise comply with health, safety, environmental and
other laws and regulations.
  We could encounter significant opposition to our refining operations at our California refineries.
  Certain of our facilities are located in areas that have a history of earthquakes or hurricanes,
the occurrence of which could materially impact our operations.
  Terrorist attacks, threats of war or actual war may negatively affect our operations, financial
condition, results of operations and prospects.
  32




---



##### 



The occurrence of a release of hazardous materials or a catastrophic event affecting our California
refineries could endanger persons living nearby.
  Covenants in our debt instruments could limit our ability to undertake certain types of
transactions and adversely affect our liquidity.
  Our insurance policies do not cover all losses, costs or liabilities that we may experience.
  We are exposed to risks associated with the credit-worthiness of the insurer of our environmental
policies.
  If we lose any of our key personnel, our ability to manage our business and continue our growth
could be negatively affected.
  33




---



##### 



A substantial portion of our Big Spring refining workforce is unionized, and we may face labor
disruptions that would interfere with our operations.
  We conduct our convenience store business under a license agreement with 7-Eleven, and the loss of
this license could adversely affect the results of operations of our retail and branded marketing
segment.
  We may not be able to successfully execute our strategy of growth through acquisitions.
  
    
    diversion of management time and attention from our existing business;
    
    challenges in managing the increased scope, geographic diversity and complexity of
operations;
    
    difficulties in integrating the financial, technological and management standards,
processes, procedures and controls of an acquired business with those of our existing
operations;
    
    liability for known or unknown environmental conditions or other contingent liabilities
not covered by indemnification or insurance;
    
    greater than anticipated expenditures required for compliance with environmental or
other regulatory standards or for investments to improve operating results;
    
    difficulties in achieving anticipated operational improvements;
    
    incurrence of additional indebtedness to finance acquisitions or capital expenditures
relating to acquired assets; and
    
    issuance of additional equity, which could result in further dilution of the ownership
interest of existing stockholders.
  34




---



##### 



We depend upon our subsidiaries for cash to meet our obligations and pay any dividends, and we do
not own 100% of the stock of our operating subsidiaries.
    It may be difficult to serve process on or enforce a United States judgment against certain of our
directors.
  
 ITEM 1B. UNRESOLVED STAFF COMMENTS.
  
 ITEM 3. LEGAL PROCEEDINGS.
  
 ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS.
  35




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##### 



PART II
 
 ITEM 5. MARKET FOR REGISTRANTS COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASE OF
EQUITY SECURITIES.
 Market Information
   Quarterly Period
    
    High
    
    Low2008Fourth Quarter
    
    $
    14.91
    
    
    $
    6.19Third Quarter
    
    
    17.00
    
    
    
    7.31Second Quarter
    
    
    17.85
    
    
    
    11.31First Quarter
    
    
    27.88
    
    
    
    11.622007Fourth Quarter
    
    $
    38.81
    
    
    $
    26.19Third Quarter
    
    
    47.10
    
    
    
    29.35Second Quarter
    
    
    45.62
    
    
    
    34.75First Quarter
    
    
    37.50
    
    
    
    24.10
 Holders
  Dividends
        36




---



##### 



Recent Sales of Unregistered Securities
  Purchases of Equity Securities by the Issuer and Affiliated Purchasers
  Stockholder Return Performance Graph
  
 37




---



##### 



ITEM 6. SELECTED FINANCIAL DATA.
    Year Ended December 31,2008
    
    
    2007
    
    
    2006
    
    
    2005
    
    
    2004(dollars in thousands, except per share data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    5,156,706
    
    
    $
    4,542,151
    
    
    $
    3,093,890
    
    
    $
    2,330,334
    
    
    $
    1,709,117Operating costs and expenses (1)
    
    
    5,258,153
    
    
    
    4,363,238
    
    
    
    2,877,811
    
    
    
    2,180,162
    
    
    
    1,639,853Gain on involuntary conversion
of assets (2)
    
    
    279,680
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Gain on disposition of assets (3)
    
    
    45,244
    
    
    
    7,206
    
    
    
    63,255
    
    
    
    38,591
    
    
    
    175Operating income
    
    
    223,477
    
    
    
    186,119
    
    
    
    279,334
    
    
    
    188,763
    
    
    
    69,439Net income
    
    
    82,883
    
    
    
    103,936
    
    
    
    157,368
    
    
    
    103,988
    
    
    
    25,132Earnings per share, basic (4)
    
    $
    1.77
    
    
    $
    2.22
    
    
    $
    3.37
    
    
    $
    2.61
    
    
    $
    0.72Weighted average shares
outstanding, basic (4)
    
    
    46,788
    
    
    
    46,763
    
    
    
    46,738
    
    
    
    39,889
    
    
    
    35,001Earnings per share, diluted
    
    $
    1.72
    
    
    $
    2.16
    
    
    $
    3.36
    
    
    $
    2.61
    
    
    $
    0.72Weighted average shares
outstanding, diluted
    
    
    49,583
    
    
    
    46,804
    
    
    
    46,779
    
    
    
    39,908
    
    
    
    35,001Cash dividends per common share
    
    
    0.16
    
    
    
    0.16
    
    
    
    3.03
    
    
    
    1.96
    
    
    
    CASH FLOW DATA:Net cash provided by (used in):Operating activities
    
    $
    (812
    )
    
    $
    123,950
    
    
    $
    142,977
    
    
    $
    137,895
    
    
    $
    76,743Investing activities
    
    
    (610,322
    )
    
    
    (147,254
    )
    
    
    (421,070
    )
    
    
    (106,962
    )
    
    
    (39,886
    )Financing activities
    
    
    560,973
    
    
    
    27,753
    
    
    
    205,439
    
    
    
    42,530
    
    
    
    19,244BALANCE SHEET DATA
(end of period):Cash and cash equivalents and
short-term investments
    
    $
    18,454
    
    
    $
    95,911
    
    
    $
    64,166
    
    
    $
    322,140
    
    
    $
    63,357Working
capital (5)
    
    
    278,781
    
    
    
    290,734
    
    
    
    235,518
    
    
    
    280,483
    
    
    
    60,558Total assets
    
    
    2,413,433
    
    
    
    1,581,386
    
    
    
    1,408,785
    
    
    
    758,780
    
    
    
    472,516Total debt
    
    
    1,103,569
    
    
    
    536,615
    
    
    
    498,669
    
    
    
    132,390
    
    
    
    187,706Stockholders equity
    
    
    431,919
    
    
    
    387,767
    
    
    
    290,330
    
    
    
    279,493
    
    
    
    71,472
 
 (1)
    
    Our buy/sell arrangements involve linked purchases and sales related to refined product
contracts entered into to address location, quality or grade requirements. As of January 1,
2006, these buy/sell transactions are included on a net basis in sales in the consolidated
statements of operations and profits are recognized when the 38




---



##### 



exchanged product is sold. Prior to January 1, 2006, the results of these buy/sell transactions
were recorded separately in sales and cost of sales in the consolidated statements of
operations. See Note 2 to our consolidated financial statements included elsewhere in this
Annual Report on Form 10-K.(2)
    
    Gain on involuntary conversion of assets reported in 2008 of $279.7 million represents the
insurance proceeds received as a result of the Big Spring refinery fire in excess of the book
value of the assets impaired of $25.3 million and demolition and repair expenses of $25.0
million incurred through December 31, 2008.(3)
    
    Gain on disposition of assets reported in 2008 primarily reflects the recognition of all the
remaining deferred gain associated with the HEP transaction due to the termination of an
indemnification agreement with HEP. Gain on disposition of assets reported in 2007 reflects
the recognition of $7.2 million deferred gain recorded primarily in connection with the HEP
transaction. Gain on disposition of assets reported in 2006 reflects the $52.5 million gain
recognized in connection with the Amdel and White Oil transaction and the recognition of $10.8
million deferred gain recorded in connection with the HEP transaction.(4)
    
    Basic weighted average shares outstanding and basic earnings per share amounts for the
periods presented reflect the effect of a 33,600-for-one split of our common stock which was
effected on July 6, 2005. On August 2, 2005, we completed an initial public offering of
11,730,000 shares of our common stock. The shares issued in our initial public offering are
included in the number of weighted average shares outstanding at December 31, 2008, 2007 and
2006, respectively.(5)
    
    Working capital excludes the current portion of long-term debt which is included as part of total debt. 39




---



##### 



ITEM 7.
    
    MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS.
 The following discussion of our financial condition and results of operations is provided as a
supplement to, and should be read in conjunction with, our consolidated financial statements and
the notes thereto included elsewhere in this Annual Report on Form 10-K and the other sections of
this Annual Report on Form 10-K , including Items 1 and 2 Business and Properties, and Item 6
Selected Financial Data.
 Forward-Looking Statements
    
    
    changes in general economic conditions and capital markets;
    
    changes in the underlying demand for our products;
    
    the availability, costs and price volatility of crude oil, other refinery feedstocks
and refined products;
    
    changes in the sweet/sour spread;
    
    changes in the light/heavy spread;
    
    the effects of transactions involving forward contracts and derivative instruments;
    
    actions of customers and competitors;
    
    changes in fuel and utility costs incurred by our facilities;
    
    disruptions due to equipment interruption, pipeline disruptions or failure at our or
third-party facilities;
    
    the execution of planned capital projects;
    
    adverse changes in the credit ratings assigned to our trade credit and debt
instruments;
    
    the effects of and cost of compliance with current and future state and federal
environmental, economic, safety and other laws, policies and regulations;
    
    operating hazards, natural disasters, casualty losses and other matters beyond our
control;
    
    our planned projects to bring back online the naphtha hydrotreater and the design and
construction of a
 40




---



##### 



hydrocracker unit at our California refineries may not be completed
within the expected time frames or within the budgeted costs for such projects due to
factors outside of our control;
    
    the global financial crisis impact on our business and financial condition in ways
that we currently cannot predict. We may face significant challenges if conditions in the
financial markets do not improve or continue to worsen, such as adversely impacting our
ability to refinance existing credit facilities or extend their terms; and
    
    the other factors discussed under Item 1A Risk Factors.
  Overview
   Refining and Unbranded Marketing Segment
    41




---



##### 



Asphalt Segment
 Retail and Branded Marketing Segment
 Summary of 2008 Developments
     2008 Operations Highlights
  42




---



##### 




    
    Operating income was $223.5 million, compared to operating income of $186.1 million in
2007. Operating income increased for 2008 over 2007 primarily due to a $279.7 million gain
on involuntary conversion of assets and a $55.0 million business interruption recovery
related to the Big Spring refinery fire.
    
    We incurred $56.9 million of costs associated with the Big Spring refinery fire.
    
    On July 3, 2008, we completed the acquisition of all the capital stock of the refinery
business located in Krotz Springs, Louisiana, from Valero Energy Corporation (Valero).
The purchase price was $333.0 million in cash plus $141.5 million representing a working
capital settlement.
    
    The combined refineries throughput for 2008 averaged 127,076 bpd, consisting of 37,793
bpd at the Big Spring refinery, 31,099 bpd at the California refineries and 58,184 bpd at
the Krotz Springs refinery as compared to the combined refineries throughput average of
129,907 bpd for 2007, consisting of 68,145 bpd at the Big Spring refinery and 61,762 bpd at
the California refineries. The California refineries throughput for 2008 was reduced to
optimize our refining and asphalt economics.
    
    The Krotz Springs refinery throughput was affected by electrical outages and reduced
crude supply due to hurricanes Gustav and Ike.
    
    Our average refinery operating margin for the Big Spring refinery decreased $16.01 per
barrel to ($3.18) per barrel for 2008, compared to $12.83 per barrel for 2007. This
decrease resulted primarily from lower refinery light product yields as a result of the
fire at the Big Spring refinery. Gulf Coast 3-2-1 average crack spreads decreased to
$10.47 per barrel for 2008 compared to $15.00 per barrel for 2007.
    
    The Big Spring refinery operated in a hydroskimming mode during most of 2008 due to the
fire on February 18, 2008, which resulted in lower refinery light product yields. Light
product yields were approximately 70% for 2008 compared to approximately 83% for 2007. The
Big Spring refinerys utilization was 52.3% in 2008 compared to 92.5% in 2007.
    
    Our California refineries operating margin decreased in 2008 by $1.08 per barrel to
$1.65 per barrel, compared to $2.73 per barrel in 2007. The decrease was primarily
attributable to a 92.4% decrease in the West Coast 6/1/2/3 crack spread to $0.48 per barrel
for 2008 from $6.33 per barrel for 2007 and from optimizing inventory levels.
    
    Asphalt margins in 2008 averaged $113.43 per ton compared to an average of $26.07 per
ton in 2007. This increase resulted primarily from a 49.4% increase in sales prices which
were $498.63 per ton for 2008 compared to $333.65 per ton for 2007.
    
    A mark-to-market adjustment was recorded of $117,452 related to the discontinuance of
cash flow hedge accounting.
 43




---



##### 



Major Influences on Results of Operations
 Refining and Unbranded Marketing
   44




---



##### 



Asphalt
 45




---



##### 



Retail and Branded Marketing
 Factors Affecting Comparability
  Big Spring Refinery Fire
    Amdel and White Oil Pipeline Transaction
  Retail Store Acquisitions
   46




---



##### 



Refinery Acquisitions
    Unscheduled Turnaround and Reduced Crude Oil Throughput
   Hurricane Activity
  HEP Transaction
  47




---



##### 



Results of Operations
 Net Sales
  Cost of Sales
 Direct Operating Expenses
 Selling, General and Administrative Expenses
 Summary Financial Tables
 48




---



##### 



ALON USA ENERGY, INC. CONSOLIDATED
 Year Ended December 31,2008
    
    
    2007
    
    
    2006(dollars in thousands, except per share data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    5,156,706
    
    
    $
    4,542,151
    
    
    $
    3,093,890Operating costs and expenses:Cost of sales
    
    
    4,853,195
    
    
    
    3,999,287
    
    
    
    2,627,321Direct operating expenses
    
    
    216,498
    
    
    
    201,196
    
    
    
    129,277Selling, general and administrative expenses (2)
    
    
    119,852
    
    
    
    105,352
    
    
    
    86,939Net costs associated with fire (3)
    
    
    56,854
    
    
    
    
    
    
    
    Business interruption recovery (4)
    
    
    (55,000
    )
    
    
    
    
    
    
    Depreciation and amortization (5)
    
    
    66,754
    
    
    
    57,403
    
    
    
    34,274Total operating costs and expenses
    
    
    5,258,153
    
    
    
    4,363,238
    
    
    
    2,877,811Gain on involuntary conversion of assets (6)
    
    
    279,680
    
    
    
    
    
    
    
    Gain on disposition of assets (7)
    
    
    45,244
    
    
    
    7,206
    
    
    
    63,255Operating income
    
    
    223,477
    
    
    
    186,119
    
    
    
    279,334Interest expense (8)
    
    
    (67,550
    )
    
    
    (47,747
    )
    
    
    (30,658
    )Equity earnings (losses) of investees
    
    
    (1,522
    )
    
    
    11,177
    
    
    
    3,161Other income, net
    
    
    1,500
    
    
    
    6,565
    
    
    
    7,740Income before income tax expense, minority interest in
income of subsidiaries and accumulated dividends on
preferred stock of subsidiary
    
    
    155,905
    
    
    
    156,114
    
    
    
    259,577Income tax expense
    
    
    62,781
    
    
    
    46,199
    
    
    
    93,968Income before minority interest in income of subsidiaries
and accumulated dividends on preferred stock of subsidiary
    
    
    93,124
    
    
    
    109,915
    
    
    
    165,609Minority interest in income of subsidiaries
    
    
    5,941
    
    
    
    5,979
    
    
    
    8,241Accumulated dividends on preferred stock of subsidiary
    
    
    4,300
    
    
    
    
    
    
    
    Net income
    
    $
    82,883
    
    
    $
    103,936
    
    
    $
    157,368Earnings per share, basic
    
    $
    1.77
    
    
    $
    2.22
    
    
    $
    3.37Weighted average shares outstanding, basic (in thousands)
    
    
    46,788
    
    
    
    46,763
    
    
    
    46,738Earnings per share, diluted
    
    $
    1.72
    
    
    $
    2.16
    
    
    $
    3.36Weighted average shares outstanding, diluted (in thousands)
    
    
    49,583
    
    
    
    46,804
    
    
    
    46,779Cash dividends per share
    
    $
    0.16
    
    
    $
    0.16
    
    
    $
    3.03CASH FLOW DATA:Net cash provided by (used in):Operating activities
    
    $
    (812
    )
    
    $
    123,950
    
    
    $
    142,977Investing activities
    
    
    (610,322
    )
    
    
    (147,254
    )
    
    
    (421,070
    )Financing activities
    
    
    560,973
    
    
    
    27,753
    
    
    
    205,439BALANCE SHEET DATA (end of period):Cash and cash equivalents and short-term investments
    
    $
    18,454
    
    
    $
    95,911
    
    
    $
    64,166Working
capital (9)
    
    
    278,781
    
    
    
    290,734
    
    
    
    235,518Total assets
    
    
    2,413,433
    
    
    
    1,581,386
    
    
    
    1,408,785Total debt
    
    
    1,103,569
    
    
    
    536,615
    
    
    
    498,669Total stockholders equity, minority interest in
subsidiaries and preferred stock of subsidiary including
accumulated dividends
    
    
    536,867
    
    
    
    403,922
    
    
    
    299,862OTHER DATA:Adjusted
EBITDA (10)
    
    $
    244,965
    
    
    $
    254,058
    
    
    $
    261,254Capital
expenditures (11)
    
    
    62,356
    
    
    
    42,204
    
    
    
    39,832Capital expenditures to rebuild the Big Spring refinery
    
    
    362,178
    
    
    
    
    
    
    
    Capital expenditures for turnaround and chemical catalyst
    
    
    9,958
    
    
    
    9,842
    
    
    
    3,940
 49




---



##### 



(1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $37.5 million,
$35.8 million, and $29.1 million for the years ended December 31, 2008, 2007 and 2006,
respectively.(2)
    
    Includes corporate headquarters selling, general and administrative expenses of $0.6 million,
$0.5 million and $0.5 million for the years ended December 31, 2008, 2007 and 2006,
respectively, which are not allocated to our three operating segments(3)
    
    Includes $51.1 million for the year ended December 31, 2008 of expenses incurred from
pipeline commitment deficiencies, crude sale losses and other incremental costs; $5.0 million
for our third party liability insurance deductible under the insurance policy; and
depreciation for the temporarily idled facilities of $0.8 million.(4)
    
    Business interruption recovery of $55.0 million was recorded for the year ended December 31,
2008 as a result of the Big Spring refinery fire with all insurance proceeds received in 2008
and January 2009.(5)
    
    Includes corporate depreciation and amortization of $0.9 million, $0.9 million and $1.6
million for the years ended December 31, 2008, 2007 and 2006, respectively, which are not
allocated to our three operating segments.(6)
    
    A gain on involuntary conversion of assets has been recorded of $279.7 million for the
insurance proceeds received in excess of the book value of the assets impaired of $25.3
million and demolition and repair expenses of $25.0 million incurred through December 31, 2008
as a result of the Big Spring refinery fire.(7)
    
    Gain on disposition of assets reported in 2008 primarily includes the recognition of deferred
gain recorded in connection with the contribution of certain product pipelines and terminals
to Holly Energy Partners, LP, (HEP), in March 2005 (HEP transaction). A recognized gain
of $42.9 million in 2008 represented all the remaining deferred gain associated with the HEP
transaction and was due to the termination of an indemnification agreement with HEP. Gain on
disposition of assets reported in 2007 reflects the recognition of $7.2 million deferred gain
recorded primarily in connection with the HEP transaction. Gain on disposition of assets
reported in 2006 reflects the $52.5 million pre-tax gain recognized in connection with the
Amdel and White Oil transaction and the recognition of $10.8 million deferred gain recorded
primarily in connection with the HEP transaction.(8)
    
    Interest expense for the year ended December 31, 2006 includes $3.6 million of prepayment
premiums and $6.1 million of unamortized debt issuance costs written off as a result of
prepayments of $100.0 million of  term debt in January 2006 and $30.2 million of retail debt in
July 2006.(9)
    
    Working capital excludes the current portion of long-term debt which is included as part of total debt.(10)
    
    See  Reconciliation of Amounts Reported Under Generally Accepted Accounting Principles
for information regarding our definition of Adjusted EBITDA, its limitations as an analytical
tool and a reconciliation of net income to Adjusted EBITDA for the periods presented.(11)
    
    Includes corporate capital expenditures of $1.2 million, $1.6 million and $0.2 million for
the years ended December 31, 2008, 2007 and 2006, respectively, which are not included in our
three operating segment capital expenditures. 50




---



##### 



REFINING AND UNBRANDED MARKETING SEGMENT (A)
 Year Ended December 31,2008
    
    
    2007
    
    
    2006(dollars in thousands, except per barrel data and pricing statistics)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    3,905,498
    
    
    $
    3,325,090
    
    
    $
    1,827,503Operating costs and expenses:Cost of sales
    
    
    3,858,823
    
    
    
    2,948,710
    
    
    
    1,483,391Direct operating expenses
    
    
    173,142
    
    
    
    154,267
    
    
    
    108,673Selling, general and administrative expenses
    
    
    17,784
    
    
    
    20,071
    
    
    
    13,399Net costs associated with fire (2)
    
    
    56,854
    
    
    
    
    
    
    
    Business interruption recovery (3)
    
    
    (55,000
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    50,047
    
    
    
    44,107
    
    
    
    24,209Total operating costs and expenses
    
    
    4,101,650
    
    
    
    3,167,155
    
    
    
    1,629,672Gain on involuntary conversion of assets (4)
    
    
    279,680
    
    
    
    
    
    
    
    Gain on disposition of assets (5)
    
    
    45,244
    
    
    
    7,138
    
    
    
    63,285Operating income
    
    $
    128,772
    
    
    $
    165,073
    
    
    $
    261,116KEY OPERATING STATISTICS AND OTHER DATA:Total sales volume (bpd)
    
    
    119,195
    
    
    
    91,027
    
    
    
    89,567Per barrel of throughput:Refinery operating margin  Big Spring (6)
    
    $
    (3.18
    )
    
    $
    12.83
    
    
    $
    12.80Refinery operating margin  CA Refineries
(6) (8)
    
    
    1.65
    
    
    
    2.73
    
    
    
    5.70Refinery operating margin  Krotz Springs
(6) (8)
    
    
    7.25
    
    
    
    N/A
    
    
    
    N/ARefinery direct operating expense  Big
Spring (7)
    
    
    4.40
    
    
    
    3.67
    
    
    
    3.63Refinery direct operating expense  CA
Refineries (7) (8)
    
    
    5.81
    
    
    
    2.79
    
    
    
    2.38Refinery direct operating expense  Krotz
Springs (7) (8)
    
    
    4.30
    
    
    
    N/A
    
    
    
    N/ACapital expenditures
    
    
    57,576
    
    
    
    28,669
    
    
    
    26,539Capital expenditures to rebuild the Big Spring
refinery
    
    
    362,178
    
    
    
    
    
    
    
    Capital expenditures for turnaround and
chemical catalyst
    
    
    9,958
    
    
    
    9,842
    
    
    
    3,940PRICING STATISTICS:WTI crude oil (per barrel)
    
    $
    99.56
    
    
    $
    72.32
    
    
    $
    66.06WTS crude oil (per barrel)
    
    
    95.78
    
    
    
    67.32
    
    
    
    60.91MAYA crude oil (per barrel)
    
    
    83.93
    
    
    
    59.86
    
    
    
    51.26Crack spreads (3/2/1) (per barrel):Gulf Coast
    
    $
    10.47
    
    
    $
    15.00
    
    
    $
    12.48Group III
    
    
    11.15
    
    
    
    19.41
    
    
    
    14.37West Coast
    
    
    15.80
    
    
    
    27.37
    
    
    
    24.30Crack spreads (6/1/2/3) (per barrel):West Coast
    
    $
    0.48
    
    
    $
    6.33
    
    
    $
    3.66Crack spreads (2/1/1) (per barrel):Gulf Coast high sulfur diesel
    
    $
    11.28
    
    
    $
    14.29
    
    
    $
    10.31Crude oil differentials (per barrel):WTI less WTS
    
    $
    3.78
    
    
    $
    5.00
    
    
    $
    5.15WTI less MAYA
    
    
    15.63
    
    
    
    12.46
    
    
    
    14.74Product price (per gallon):Gulf Coast unleaded gasoline
    
    
    247.1¢
    
    
    
    204.5¢
    
    
    
    182.9¢Gulf Coast ultra low-sulfur diesel
    
    
    291.8
    
    
    
    214.7
    
    
    
    195.1Group III unleaded gasoline
    
    
    248.1
    
    
    
    216.0
    
    
    
    186.6Group III ultra low-sulfur diesel
    
    
    294.5
    
    
    
    223.3
    
    
    
    201.4West Coast LA CARBOB (unleaded gasoline)
    
    
    267.9
    
    
    
    244.2
    
    
    
    219.6West Coast LA ultra low-sulfur diesel
    
    
    288.3
    
    
    
    223.7
    
    
    
    206.0Natural gas (per MMBTU)
    
    $
    8.90
    
    
    $
    7.12
    
    
    $
    6.98
 
 (A)
    
    In the first quarter of 2008, our branded marketing business was removed from the refining and
marketing segment and combined with the retail segment. Information for prior periods has been
recast to provide a comparison to the current year results. 51




---



##### 



Year Ended December 31,2008
    
    
    2007
    
    
    2006bpd
    
    
    %
    
    
    bpd
    
    
    %
    
    
    bpd
    
    
    %THROUGHPUT AND PRODUCTION DATA:Big Spring refineryRefinery throughput:Sour crude
    
    
    31,654
    
    
    
    83.8
    
    
    
    58,607
    
    
    
    86.0
    
    
    
    58,529
    
    
    
    89.4Sweet crude
    
    
    4,270
    
    
    
    11.3
    
    
    
    5,017
    
    
    
    7.4
    
    
    
    2,987
    
    
    
    4.6Blendstocks
    
    
    1,869
    
    
    
    4.9
    
    
    
    4,521
    
    
    
    6.6
    
    
    
    3,897
    
    
    
    6.0Total refinery throughput (9)
    
    
    37,793
    
    
    
    100.0
    
    
    
    68,145
    
    
    
    100.0
    
    
    
    65,413
    
    
    
    100.0Refinery production:Gasoline
    
    
    14,266
    
    
    
    38.4
    
    
    
    32,135
    
    
    
    47.5
    
    
    
    29,671
    
    
    
    46.0Diesel/jet
    
    
    10,439
    
    
    
    28.2
    
    
    
    19,676
    
    
    
    29.1
    
    
    
    20,651
    
    
    
    32.0Asphalt
    
    
    4,850
    
    
    
    13.1
    
    
    
    7,620
    
    
    
    11.3
    
    
    
    6,147
    
    
    
    9.5Petrochemicals
    
    
    1,221
    
    
    
    3.3
    
    
    
    3,980
    
    
    
    5.9
    
    
    
    4,465
    
    
    
    6.9Other
    
    
    6,298
    
    
    
    17.0
    
    
    
    4,190
    
    
    
    6.2
    
    
    
    3,627
    
    
    
    5.6Total refinery production (10)
    
    
    37,074
    
    
    
    100.0
    
    
    
    67,601
    
    
    
    100.0
    
    
    
    64,561
    
    
    
    100.0Refinery utilization (11)
    
    
    
    
    
    
    52.3
    %
    
    
    
    
    
    
    92.5
    %
    
    
    
    
    
    
    90.8
    %Year Ended December 31,2008
    
    
    2007
    
    
    2006bpd
    
    
    %
    
    
    bpd
    
    
    %
    
    
    bpd
    
    
    %THROUGHPUT AND PRODUCTION DATA:California refineriesRefinery throughput:Medium sour crude
    
    
    8,014
    
    
    
    25.8
    
    
    
    20,839
    
    
    
    33.7
    
    
    
    37,171
    
    
    
    61.9Heavy crude
    
    
    22,590
    
    
    
    72.6
    
    
    
    40,700
    
    
    
    65.9
    
    
    
    22,533
    
    
    
    37.5Blendstocks
    
    
    495
    
    
    
    1.6
    
    
    
    223
    
    
    
    0.4
    
    
    
    362
    
    
    
    0.6Total refinery throughput (8) (9)
    
    
    31,099
    
    
    
    100.0
    
    
    
    61,762
    
    
    
    100.0
    
    
    
    60,066
    
    
    
    100.0Refinery production:Gasoline
    
    
    4,141
    
    
    
    13.7
    
    
    
    7,318
    
    
    
    12.1
    
    
    
    6,806
    
    
    
    11.6Diesel/jet
    
    
    7,481
    
    
    
    24.8
    
    
    
    13,360
    
    
    
    22.1
    
    
    
    11,026
    
    
    
    18.9Asphalt
    
    
    9,214
    
    
    
    30.5
    
    
    
    19,006
    
    
    
    31.5
    
    
    
    19,500
    
    
    
    33.3Light Unfinished
    
    
    
    
    
    
    
    
    
    
    3,071
    
    
    
    5.1
    
    
    
    6,144
    
    
    
    10.5Heavy Unfinished
    
    
    9,182
    
    
    
    30.4
    
    
    
    16,793
    
    
    
    27.9
    
    
    
    2,938
    
    
    
    5.0Other
    
    
    192
    
    
    
    0.6
    
    
    
    793
    
    
    
    1.3
    
    
    
    12,126
    
    
    
    20.7Total refinery production (8) (10)
    
    
    30,210
    
    
    
    100.0
    
    
    
    60,341
    
    
    
    100.0
    
    
    
    58,540
    
    
    
    100.0Refinery utilization (11)
    
    
    
    
    
    
    46.3
    %
    
    
    
    
    
    
    85.9
    %
    
    
    
    
    
    
    83.8
    %Period EndedDecember 31,2008bpd
    
    
    %THROUGHPUT AND PRODUCTION DATA:Krotz Springs refinery (B)Refinery throughput:Light sweet crude
    
    
    43,361
    
    
    
    74.5Heavy sweet crude
    
    
    11,979
    
    
    
    20.6Blendstocks
    
    
    2,844
    
    
    
    4.9Total refinery throughput (8) (9)
    
    
    58,184
    
    
    
    100.0Refinery production:Gasoline
    
    
    25,195
    
    
    
    42.8Diesel/jet
    
    
    26,982
    
    
    
    45.9Heavy oils
    
    
    1,402
    
    
    
    2.4Other
    
    
    5,258
    
    
    
    8.9Total refinery production (8) (10)
    
    
    58,837
    
    
    
    100.0Refinery utilization (11)
    
    
    
    
    
    
    66.6
    %
 
 (B)
    
    The period ended December 31, 2008, represents throughput and production data for the
period from July 1, 2008 through December 31, 2008. 52




---



##### 



(1)
    
    Net sales include inter-segment sales to our asphalt and retail and branded marketing
segments at prices which
are intended to approximate wholesale market prices. These inter-segment sales are eliminated
through consolidation of our financial statements. Net sales for the year ended 2006 include
$3.3 million for the sale of sulfur credits. Following the acquisition of Paramount Petroleum
Corporation and Edgington Oil Company, we notified the Environmental Protection Agency that we
no longer qualify as a small refiner which will limit our ability to generate sulfur credits
in the future.(2)
    
    Includes $51.1 million for the year ended December 31, 2008 of expenses incurred from
pipeline commitment deficiencies, crude sale losses and other incremental costs; $5.0 million
for our third party liability insurance deductible under the insurance policy; and
depreciation for the temporarily idled facilities of $0.8 million.(3)
    
    Business interruption recovery of $55.0 million was recorded for the year ended December 31,
2008 as a result of the Big Spring refinery fire with all insurance proceeds received in 2008
and January 2009.(4)
    
    A gain on involuntary conversion of assets has been recorded of $279.7 million for the
insurance proceeds received in excess of the book value of the assets impaired of $25.3
million and demolition and repair expenses of $25.0 million incurred through December 31, 2008
as a result of the Big Spring refinery fire.(5)
    
    Gain on disposition of assets reported in 2008 primarily includes the recognition of deferred
gain recorded in connection with HEP transaction. A recognized gain of $42.9 million
represented all the recognition of the remaining deferred gain associated with the HEP
transaction and was due to the termination of an indemnification agreement with HEP. Gain on
disposition of assets reported in 2007 reflects the recognition of $7.1 million deferred gain
recorded primarily in connection with the HEP transaction. Gain on disposition of assets
reported in 2006 reflects the $52.5 million pre-tax gain recognized in connection with the
Amdel and White Oil transaction and the recognition of $10.8 million deferred gain recorded
primarily in connection with the HEP transaction.(6)
    
    Refinery operating margin is a per barrel measurement calculated by dividing the margin
between net sales and cost of sales (exclusive of unrealized hedging gains and losses and
inventories adjustments related to acquisitions) attributable to each refinery by the
refinerys throughput volumes. Industry-wide refining results are driven and measured by the
margins between refined product prices and the prices for crude oil, which are referred to as
crack spreads. We compare our refinery operating margins to these crack spreads to assess our
operating performance relative to other participants in our industry. There were unrealized
hedging gains of $4.2 million for the year ended December 31, 2008 and unrealized hedging
losses of $4.3 million and $0.3 million for the California refineries for the years ended
December 31, 2007 and 2006, respectively. There were unrealized hedging gains of $117.5
million for the Krotz Springs refinery for the six months ended December 31, 2008. The 2008
refinery operating margin for the Krotz Springs refinery excludes a charge of $127.4 million
to cost of sales for inventories adjustments related to the acquisition. The 2006 refinery
operating margin for the California refineries excludes a charge of $20.0 million to cost of
sales for inventories adjustments related to acquisitions.(7)
    
    Refinery direct operating expense is a per barrel measurement calculated by dividing direct
operating expenses at our Big Spring, California, and Krotz Springs refineries, exclusive of
depreciation and amortization, by the applicable refinerys total throughput volumes.(8)
    
    Total refinery throughput and production data for 2008 includes our Krotz Springs refinery
for the period from July 1, 2008 through December 31, 2008. Total refinery throughput and
production data for 2006 includes our Paramount refinery for the period from August 1, 2006
through December 31, 2006 and our Long Beach refinery for the period from September 28, 2006
through December 31, 2006.(9)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock
inputs in the refinery production process.(10)
    
    Total refinery production represents the barrels per day of various products produced from
processing crude and other refinery feedstocks through the crude units and other conversion
units at the refineries. Light product yields decreased at the Big Spring refinery for the
year ended December 31, 2008 due to the fire on February 18, 2008 and the re-start of the
crude unit in a hydroskimming mode on April 5, 2008.(11)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds. The decrease
in refinery utilization at our Big Spring refinery for 2008 is due to the fire on February 18,
2008. Production ceased at the Big Spring refinery until the re-start of the crude unit in a
hydroskimming mode on April 5, 2008. The Big Spring refinery returned to a normal operating
mode with the re-start of the Fluid Catalytic Cracking Unit (FCCU) on September 26, 2008.
The decrease in refinery utilization at our California refineries is due to reduced throughput
to optimize
our refining and asphalt economics. The low refinery utilization at our Krotz Springs refinery
is due to shutdowns during hurricanes Gustav and Ike and limited crude supply and electrical
outages following the hurricanes.  53




---



##### 



ASPHALT SEGMENT
 Year Ended December 31,2008
    
    
    2007
    
    
    2006(dollars in thousands, except per ton data)STATEMENT OF OPERATIONS DATA:Net sales
    
    $
    647,221
    
    
    $
    642,937
    
    
    $
    389,634Operating costs and expenses:Cost of sales (1)
    
    
    499,992
    
    
    
    592,709
    
    
    
    346,839Direct operating expenses
    
    
    43,356
    
    
    
    46,929
    
    
    
    20,604Selling, general and administrative expenses
    
    
    4,292
    
    
    
    2,825
    
    
    
    8,773Depreciation and amortization
    
    
    2,139
    
    
    
    2,145
    
    
    
    2,247Total operating costs and expenses
    
    
    549,779
    
    
    
    644,608
    
    
    
    378,463Operating income (loss)
    
    $
    97,442
    
    
    $
    (1,671
    )
    
    $
    11,171KEY OPERATING STATISTICS AND OTHER DATA:Number of terminals (end of period)
    
    
    12
    
    
    
    12
    
    
    
    12Total sales volume (in thousands)
    
    
    1,298
    
    
    
    1,927
    
    
    
    1,153Sales price per ton
    
    $
    498.63
    
    
    $
    333.65
    
    
    $
    337.93Asphalt margin per ton (2)
    
    $
    113.43
    
    
    $
    26.07
    
    
    $
    37.12Capital expenditures
    
    $
    644
    
    
    $
    2,167
    
    
    $
    3,156
 
 (1)
    
    Cost of sales includes intersegment purchases of asphalt blends and motor fuels from our
refining and unbranded marketing segment at prices which approximate wholesale market prices.
These intersegment purchases are eliminated through consolidation of our financial statements.(2)
    
    Asphalt margin is a per ton measurement calculated by dividing the margin between net sales
and cost of sales by the total sales volume. Asphalt margins are used in the asphalt industry
to measure operating results related to asphalt sales. 54




---



##### 



RETAIL AND BRANDED MARKETING SEGMENT (A)
 Year Ended December 31,2008
    
    
    2007
    
    
    2006(dollars in thousands, except per gallon data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    1,227,319
    
    
    $
    1,274,516
    
    
    $
    1,264,593Operating costs and expenses:Cost of sales (2)
    
    
    1,117,712
    
    
    
    1,158,260
    
    
    
    1,184,931Selling, general and administrative expenses
    
    
    97,172
    
    
    
    81,933
    
    
    
    64,256Depreciation and amortization
    
    
    13,674
    
    
    
    10,245
    
    
    
    6,205Total operating costs and expenses
    
    
    1,228,558
    
    
    
    1,250,438
    
    
    
    1,255,392Gain (loss) on disposition of assets
    
    
    
    
    
    
    68
    
    
    
    (30
    )Operating income (loss)
    
    $
    (1,239
    )
    
    $
    24,146
    
    
    $
    9,171KEY OPERATING STATISTICS AND OTHER DATA:Integrated branded fuel sales (thousands of gallons) (3)
    
    
    225,474
    
    
    
    254,044
    
    
    
    268,574Integrated branded fuel margin (cents per gallon) (3)
    
    
    4.4
    ¢
    
    
    9.2
    ¢
    
    
    5.8
    ¢Non-Integrated branded fuel sales (thousands of gallons) (3)
    
    
    113,626
    
    
    
    204,537
    
    
    
    275,214Non-Integrated branded fuel margin (cents per gallon) (3)
    
    
    (0.3
    ) ¢
    
    
    1.3
    ¢
    
    
    (0.6
    ) ¢Number of stores (end of period)
    
    
    306
    
    
    
    307
    
    
    
    206Retail fuel sales (thousands of gallons)
    
    
    96,974
    
    
    
    91,946
    
    
    
    75,969Retail fuel sales (thousands of gallons per site per month) (4)
    
    
    27
    
    
    
    30
    
    
    
    34Retail fuel margin (cents per gallon) (5)
    
    
    19.7
    ¢
    
    
    21.2
    ¢
    
    
    19.2
    ¢Retail fuel sales price (dollar per gallon) (6)
    
    $
    3.26
    
    
    $
    2.82
    
    
    $
    2.55Merchandise sales
    
    $
    261,144
    
    
    $
    220,807
    
    
    $
    157,155Merchandise sales (per site per month) (4)
    
    
    72
    
    
    
    72
    
    
    
    70Merchandise margin (7)
    
    
    30.9
    %
    
    
    32.0
    %
    
    
    32.5
    %Capital expenditures
    
    $
    2,928
    
    
    $
    9,797
    
    
    $
    9,949
 
 (A)
    
    In the first quarter of 2008, our branded marketing business was removed from the refining and
marketing segment and combined with the retail segment. Information for prior periods has been
recast to provide a comparison to the current year results.(1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $37.5 million,
$35.8 million, and $29.1 million for the years ended December 31, 2008, 2007 and 2006,
respectively.(2)
    
    Cost of sales includes inter-segment purchases of motor fuels from our refining and unbranded
marketing segment at prices which approximate market prices. These inter-segment purchases are
eliminated through consolidation of our financial statements.(3)
    
    Marketing sales volume represents branded fuel sales to our wholesale marketing customers
located in both our integrated and non-integrated regions. The branded fuels we sell in our
integrated region are primarily supplied by the Big Spring refinery, but due to the fire on
February 18, 2008 at the Big Spring refinery, more fuel has been purchased from third-party
suppliers. The branded fuels we sell in the non-integrated region are obtained from
third-party suppliers. The marketing margin represents the margin between the net sales and
cost of sales attributable to our branded fuel sales volume, expressed on a cents-per-gallon
basis and includes net credit card revenue from these sales.(4)
    
    Retail fuel and merchandise sales per site for 2008 were calculated using 306 stores, 2007
were calculated using 206 stores for six months and 307 stores for six months due to the
acquisition of Skinnys, Inc. on June 29, 2007. Fuel and merchandise sales per site for 2006
were calculated using 167 stores for six months and 206 stores for six months due to the Good
Time Stores acquisition on July 3, 2006.(5)
    
    Retail fuel margin represents the difference between motor fuel sales revenue and the net
cost of purchased motor fuel, including transportation costs and associated motor fuel taxes,
expressed on a cents-per-gallon basis. Motor fuel margins are frequently used in the retail
industry to measure operating results related to motor fuel sales.(6)
    
    Retail fuel sales price per gallon represents the average sales price for motor fuels sold
through our retail convenience stores.(7)
    
    Merchandise margin represents the difference between merchandise sales revenues and the
delivered cost of merchandise purchases, net of rebates and commissions, expressed as a
percentage of merchandise sales revenues. Merchandise margins, also referred to as in-store
margins, are commonly used in the retail industry to measure in-store, or non-fuel, operating
results. 55




---



##### 



Year Ended December 31, 2008 Compared to Year Ended December 31, 2007
 Net Sales
 Consolidated.
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Cost of Sales
 Consolidated
 Refining and Unbranded Marketing Segment
 56




---



##### 



Asphalt Segment
 Retail and Branded Marketing Segment
 Direct Operating Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Selling, General and Administrative Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Depreciation and Amortization
  Operating Income
 Consolidated
 57




---



##### 



Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Interest Expense
  Income Tax Expense
  Minority Interest in Income of Subsidiaries
  58




---



##### 



Net Income
  Year Ended December 31, 2007 Compared to Year Ended December 31, 2006
 Net Sales
 Consolidated.
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Cost of Sales
 Consolidated
 Refining and Unbranded Marketing Segment
 59




---



##### 



Asphalt Segment
 Retail and Branded Marketing Segment
 Direct Operating Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Selling, General and Administrative Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 60




---



##### 



Depreciation and Amortization
  Operating Income
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Interest Expense
  Income Tax Expense
 Application of FASB Statement No. 109, Accounting for Income Taxes, for
the Tax Deduction Provided to U.S. Based Manufacturers by the American Jobs Creation Act of 2004
 61




---



##### 



Minority Interest in Income of Subsidiaries
  Net Income
  Liquidity and Capital Resources
     62




---



##### 



Cash Flow
  Year Ended December 312008
    
    
    2007
    
    
    2006(dollars in thousands)Cash provided by (used in):Operating activities
    
    $
    (812
    )
    
    $
    123,950
    
    
    $
    142,977Investing activities
    
    
    (610,322
    )
    
    
    (147,254
    )
    
    
    (421,070
    )Financing activities
    
    
    560,973
    
    
    
    27,753
    
    
    
    205,439Net increase (decrease) in cash and cash equivalents
    
    $
    (50,161
    )
    
    $
    4,449
    
    
    $
    (72,654
    )
 Cash Flows Provided By Operating Activities
   Cash Flows Used In Investing Activities
   Cash Flows Provided By Financing Activities
   63




---



##### 



Cash, Cash Equivalents and Short-Term Investment Position and Indebtedness
   Summary of Indebtedness
 As of December 31, 2008Amount Outstanding
    
    
    Total Facilities
    
    
    Total Availability (1)(dollars in thousands)Debt, including current portion:Term loan
credit facilities
    
    $
    739,810
    
    
    $
    739,810
    
    
    $
    Revolving credit facilities
    
    
    276,818
    
    
    
    900,000
    
    
    
    248,187Retail credit facilities
    
    
    86,941
    
    
    
    86,941
    
    
    
    Totals
    
    $
    1,103,569
    
    
    $
    1,726,751
    
    
    $
    248,187
 
 (1)
    
    Total availability was calculated as the lesser of (a) the total size of the facilities less
outstanding borrowings and letters of credit as of December 31, 2008 which was $460.9 million,
and (b) total borrowing base, if applicable, less outstanding borrowings and letters of credit
as of December 31, 2008 which was $248.2 million. Credit Facilities
 Alon USA Energy, Inc. Credit Facilities
 Term Loan Credit Facility.
   64




---



##### 



Letters of Credit Facility.
 Alon USA, LP Credit Facilities
 Revolving Credit Facility.
   Paramount Petroleum Corporation Credit Facility
 Revolving Credit Facility.
  65




---



##### 



Alon Refining Krotz Springs, Inc. Credit Facilities
 Term Loan Credit Facility.
     Revolving Credit Facility.
       66




---



##### 



Retail Credit Facilities
      Other Retail Related Credit Facilities
   Capital Spending
  67




---



##### 



2009
    
    
    2010(dollars in thousands)Refining and Unbranded Marketing Segment:Sustaining maintenance
    
    $
    40,189
    
    
    $
    47,295Growth/profit improvement/other
    
    
    8,155
    
    
    
    8,835Chemical catalyst and turnaround
    
    
    15,396
    
    
    
    30,808Total
    
    
    63,740
    
    
    
    86,938Asphalt Segment:Sustaining maintenance
    
    
    2,746
    
    
    
    3,148Growth/profit improvement
    
    
    600
    
    
    
    1,810Total
    
    
    3,346
    
    
    
    4,958Retail and Branded Marketing Segment:Sustaining maintenance
    
    
    4,913
    
    
    
    1,724Growth/profit improvement
    
    
    4,550
    
    
    
    4,000Total
    
    
    9,463
    
    
    
    5,724Corporate Segment:Sustaining
    
    
    4,285
    
    
    
    2,675Total Capital Expenditures
    
    $
    80,833
    
    
    $
    100,295
 Clean Air Capital Expenditures
 Turnaround and Chemical Catalyst Costs
  2009
    
    
    2010
    
    
    2011
    
    
    2012
    
    
    2013(dollars in thousands)Scheduled turnaround costs
    
    $
    2,300
    
    
    $
    17,508
    
    
    $
    3,750
    
    
    $
    9,617
    
    
    $
    29,000Chemical catalyst costs
    
    
    13,096
    
    
    
    13,300
    
    
    
    11,040
    
    
    
    13,300
    
    
    
    10,000Total
    
    $
    15,396
    
    
    $
    30,808
    
    
    $
    14,790
    
    
    $
    22,917
    
    
    $
    39,000
 Contractual Obligations and Commercial Commitments
  Payments Due by PeriodLess Than
    
    
    
    
    
    
    
    
    
    
    More ThanContractual Obligations
    
    1 Year
    
    
    1-3 Years
    
    
    3-5 Years
    
    
    5 Years
    
    
    Total(dollars in thousands)Long-term debt obligations
    
    $
    28,397
    
    
    $
    169,027
    
    
    $
    197,535
    
    
    $
    708,610
    
    
    $
    1,103,569Operating lease obligations
    
    
    38,236
    
    
    
    85,134
    
    
    
    25,707
    
    
    
    65,025
    
    
    
    214,102Pipelines and Terminals Agreement (1)
    
    
    27,549
    
    
    
    82,647
    
    
    
    55,099
    
    
    
    151,572
    
    
    
    316,867Other commitments (2)
    
    
    2,827
    
    
    
    8,483
    
    
    
    5,654
    
    
    
    20,499
    
    
    
    37,463Total obligations
    
    $
    97,009
    
    
    $
    345,291
    
    
    $
    283,995
    
    
    $
    945,706
    
    
    $
    1,672,001
 
 (1)
    
    Balances represent the minimum committed volume multiplied by the tariff and terminal rates
pursuant to the terms of the Pipelines and Terminals Agreement with HEP, as well as our
minimum requirements with Sunoco.(2)
    
    Other commitments include refinery maintenance services costs.   68




---



##### 



Off-Balance Sheet Arrangements
  Critical Accounting Policies
  Inventory
 Environmental and Other Loss Contingencies
 Turnarounds and Chemical Catalyst Costs
 69




---



##### 



Impairment of Long-Lived Assets Accounting for the Impairment or Disposal of Long-Lived Assets
 Deferred Income Taxes
 Asset Retirement Obligations Accounting for Asset Retirement Obligations
  Goodwill and Intangible Assets
  70




---



##### 



New Accounting Standards and Disclosures
 Employers Disclosures about Postretirement Benefit Plans Employers Disclosures about Pensions and Other
Postretirement Benefits
 Equity Method Investment Accounting Considerations
 Accounting by Lessees
for Maintenance Deposits
 Determination of the Useful Life
of Intangible Assets Goodwill and Other
Intangible Assets.
 Disclosure about Derivative Instruments and Hedging Activities
 Fair Value
Measurements
 Partial Deferral of the
Effective Date of Statement 157
 71




---



##### 



The Fair Value Option for Financial Assets and
Financial Liabilities
 Non-controlling Interests in Consolidated
Financial Statements, an Amendment of ARB 51 (SFAS No. 160)
 Business Combinations
 Accounting for Uncertainty in Income
Taxes, an interpretation of FASB Statement No. 109
 How Taxes Collected from
Customers and Remitted to Governmental Authorities Should Be Presented in the Income Statement
(That Is, Gross versus Net Presentation)
 Reconciliation of Amounts Reported Under Generally Accepted Accounting Principles
 Reconciliation of Adjusted EBITDA to amounts reported under generally accepted accounting principles in
financial statements.
  72




---



##### 




    
    Adjusted EBITDA does not reflect our cash expenditures or future requirements for
capital expenditures or contractual commitments;
    
    Adjusted EBITDA does not reflect the interest expense or the cash requirements
necessary to service interest or principal payments on our debt;
    
    Adjusted EBITDA does not reflect the prior claim that minority stockholders have on the
income generated by non-wholly-owned subsidiaries;
    
    Adjusted EBITDA does not reflect changes in or cash requirements for our working
capital needs; and
    
    Our calculation of Adjusted EBITDA may differ from the Adjusted EBITDA calculations of
other companies in our industry, limiting its usefulness as a comparative measure.
   For the Year Ended December 31,2008
    
    
    2007
    
    
    2006(in thousands)Net income
    
    $
    82,883
    
    
    $
    103,936
    
    
    $
    157,368Minority interest in income
of subsidiaries (including
accumulated dividends on
preferred stock of
subsidiary)
    
    
    10,241
    
    
    
    5,979
    
    
    
    8,241Income tax expense
    
    
    62,781
    
    
    
    46,199
    
    
    
    93,968Interest expense
    
    
    67,550
    
    
    
    47,747
    
    
    
    30,658Depreciation and amortization
    
    
    66,754
    
    
    
    57,403
    
    
    
    34,274Gain on disposition of assets
    
    
    (45,244
    )
    
    
    (7,206
    )
    
    
    (63,255
    )Adjusted EBITDA
    
    $
    244,965
    
    
    $
    254,058
    
    
    $
    261,254
  
 ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK.
 Quantitative and Qualitative Disclosure About Market Risk
  Commodity Price Risk
  73




---



##### 



Contract
    
    Wtd AvgVolume
    
    Purchase
    
    Wtd Avg
    
    ContractDescription of Activity
    
    (in barrels)
    
    Price
    
    Sales Price
    
    Value
    
    Fair Value
    
    Gain (Loss)Forwards-short (Gasoline)
    
    
    (150,000
    )
    
    
    
    
    
    
    37.73
    
    
    
    (5,660
    )
    
    
    (6,555
    )
    
    
    (895
    )Forwards-short (Diesel)
    
    
    (50,000
    )
    
    
    
    
    
    
    55.74
    
    
    
    (2,787
    )
    
    
    (3,095
    )
    
    
    (308
    )Futures-long (Heating Oil)
    
    
    11,000
    
    
    
    57.69
    
    
    
    
    
    
    
    634
    
    
    
    666
    
    
    
    32Futures-short (Heating Oil)
    
    
    (78,000
    )
    
    
    
    
    
    
    60.07
    
    
    
    (4,685
    )
    
    
    (4,724
    )
    
    
    (39
    )Futures-short (RBOB)
    
    
    (5,000
    )
    
    
    
    
    
    
    47.29
    
    
    
    (236
    )
    
    
    (223
    )
    
    
    13
 ContractVolume
    
    Wtd Avg
    
    Wtd Avg
    
    ContractDescription of Activity
    
    (in barrels)
    
    Contract
    
    Sales Price
    
    Value
    
    Fair Value
    
    Gain (Loss)Futures-crack spread (Heating Oil)
    
    
    12,000,125
    
    
    $
    21.95
    
    
    $
    12.06
    
    
    $
    260,469
    
    
    $
    142,984
    
    
    $
    117,485Futures-long (SPR swaps)
    
    
    672,000
    
    
    
    89.34
    
    
    
    51.43
    
    
    
    60,036
    
    
    
    34,563
    
    
    
    (25,473
    )
 Interest Rate Risk
   74




---



##### 



ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA.
  
 ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE.
  
 ITEM 9A. CONTROLS AND PROCEDURES.
 Disclosure Controls and Procedures
  Managements Report on Internal Control over Financial Reporting
   Changes in Internal Control Over Financial Reporting
  Certifications
   
 ITEM 9B. OTHER INFORMATION.
  75




---



##### 



PART III
 
 ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT.
    
 ITEM 11. EXECUTIVE COMPENSATION.
  
 ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED
STOCKHOLDER MATTERS.
  
 ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS.
  
 ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES.
  76




---



##### 



PART IV
 
 ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES.
 (a)
    
    The following documents are filed as part of this report:(1)
    
    Consolidated Financial Statements and Schedule, see Index to Consolidated Financial
Statements and Schedule on page F-1.
 (a)
    
    Schedule II  Valuation and Qualifying accounts is included in the Notes to Consolidated
Financial Statements.
 (2)
    
    Exhibits: Reference is made to the Index of Exhibits immediately preceding the exhibits
hereto, which index is incorporated herein by reference.
 Exhibit No.
    
    Description of Exhibit3.1
    
    Amended and Restated Certificate of Incorporation of Alon USA Energy, Inc. (incorporated by
reference to Exhibit 3.1 to Form S-1/A, filed by the Company on July 7, 2005, SEC File No.
333-124797).3.2
    
    Amended and Restated Bylaws of Alon USA Energy, Inc. (incorporated by reference to Exhibit
3.2 to Form S-1/A, filed by the Company on July 14, 2005, SEC File No. 333-124797).4.1
    
    Specimen Common Stock Certificate (incorporated by reference to Exhibit 4.1 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.1
    
    Trademark License Agreement, dated as of July 31, 2000, among Finamark, Inc., Atofina
Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.3 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.2
    
    First Amendment to Trademark License Agreement, dated as of April 11, 2001, among Finamark,
Inc., Atofina Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.4
to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.3
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, L.P. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on February 2, 2008, SEC File No. 001-32567).10.4
    
    Pipeline Lease Agreement, dated as of February 21, 1997, between Navajo Pipeline Company and
American Petrofina Pipe Line Company (incorporated by reference to Exhibit 10.6 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.5
    
    Amendment and Supplement to Pipeline Lease Agreement, dated as of August 31, 2007, by and
between HEP Pipeline Assets, Limited Partnership and Alon USA, LP (incorporated by reference
to Exhibit 10.1 to Form 10-Q, filed by the Company on November 8, 2007).10.6
    
    Contribution Agreement, dated as of January 25, 2005, among Holly Energy Partners, L.P.,
Holly Energy Partners  Operating, L.P., T & R Assets, Inc., Fin-Tex Pipe Line Company, Alon
USA Refining, Inc., Alon Pipeline Assets, LLC, Alon Pipeline Logistics, LLC, Alon USA, Inc.
and Alon USA, LP (incorporated by reference to Exhibit 10.7 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.7
    
    Pipelines and Terminals Agreement, dated as of February 28, 2005, between Alon USA, LP and
Holly Energy Partners, L.P. (incorporated by reference to Exhibit 10.8 to Form S-1, filed by
the Company on May 11, 2005, SEC File No. 333-124797).10.8
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, LP (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
February 5, 2008, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.9
    
    Liquor License Purchase Agreement, dated as of May 12, 2003, between Southwest Convenience
Stores, LLC and SCS Beverage, Inc. (incorporated by reference to Exhibit 10.34 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.10
    
    Premises Lease, dated as of May 12, 2003, between Southwest Convenience Stores, LLC and SCS
Beverage, Inc. (incorporated by reference to Exhibit 10.35 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.11
    
    Amended Revolving Credit Agreement, dated as of January 14, 2004, among Alon USA, LP, the
guarantor companies and financial institutions identified therein and Israel Discount Bank
of New York (incorporated by reference to Exhibit 10.19 to Form S-1, filed by the Company on
May 11, 2005, SEC File No. 333-124797).10.12
    
    First Amendment, dated as of February 10, 2005, to the Amended Revolving Credit Agreement,
dated as of January 14, 2004, among Alon USA, LP, the guarantor companies and financial
institutions identified therein and Israel Discount Bank of New York (incorporated by
reference to Exhibit 10.20 to Form S-1, filed by the Company on May 11, 2005, SEC File No.
333-124797).10.13
    
    Second Amendment, dated as of June 16, 2005, to the Amended Revolving Credit Agreement,
dated as of January 14, 2004, among Alon USA, LP, the guarantor companies and financial
institutions identified therein and Israel Discount Bank of New York (incorporated by
reference to Exhibit 10.20.1 to Form S-1/A, filed by the Company on June 17, 2005, SEC File
No. 333-124797).10.14
    
    Amended Revolving Credit Agreement, dated as of February 15, 2006, among Alon USA, LP, the
guarantor companies and financial institutions named therein, Israel Discount Bank of New
York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on February 16, 2006, SEC File No. 001-32567).10.15
    
    Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.2 to Form 8-K, filed by the Company on June 26, 2006, SEC File
No. 001-32567).10.16
    
    First Amendment to Amended Revolving Credit Agreement, dated as of August 4, 2006, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.25 to Form 10-K, filed by the Company on March 15, 2007 SEC File
No. 001-32567).10.17
    
    Waiver, Consent, Partial Release and Second Amendment, dated as of February 28, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, Alon USA, LP, Edgington Oil
Company, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on March 5, 2007, SEC File No.
001-32567).10.18
    
    Third Amendment to Amended Revolving Credit Agreement, dated as of June 29, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc.,
Alon USA, LP, the guarantor companies and financial institutions named therein, Israel
Discount Bank of New York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to
Form 8-K, filed by the Company on July 20, 2007, SEC File No. 001-32567).10.19
    
    Waiver, Consent, Partial Release and Fourth Amendment, dated as of July 2, 2008, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.4 to Form 8-K, filed by the Company on July 10, 2008, SEC File
No. 001-32567).10.20
    
    Credit Agreement, dated as of June 6, 2006, among Southwest Convenience Stores, LLC, the
lenders party thereto and Wachovia Bank, National Association (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on June 7, 2006, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.21
    
    Amended and Restated Credit Agreement, dated as of June 29, 2007, among Southwest
Convenience Stores, LLC, the lenders party thereto and Wachovia Bank, National Association
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on July 2,
2007, SEC File No. 001-32567).10.22
    
    Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc., the lenders party
thereto and Credit Suisse (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by
the Company on June 26, 2006, SEC File No. 001-32567).10.23
    
    Amendment No. 1 to the Credit Agreement, dated as of February 28, 2007, by and among Alon
USA Energy, Inc., the lenders party thereto and Credit Suisse (incorporated by reference to
Exhibit 10.3 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.24
    
    Second Amended and Restated Credit Agreement, dated as of February 28, 2007, among Paramount
Petroleum Corporation, Bank of America, N.A. and certain other guarantor companies and
financial institutions from time to time named therein (incorporated by reference to Exhibit
10.1 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.25
    
    First Amendment to Second Amended and Restated Credit Agreement, dated as of March 30, 2007,
among Paramount Petroleum Corporation, Bank of America, N.A. and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.37 to Form 10-K, filed by the Company on March 11, 2008, SEC File
No. 001-32567).10.26
    
    Term Loan Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., the lenders party thereto and Credit Suisse, as
administrative agent and collateral agent (incorporated by reference to Exhibit 10.2 to Form
8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.27
    
    Loan and Security Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank of America,
N.A., as administrative agent (incorporated by reference to Exhibit 10.3 to Form 8-K, filed
by the Company on July 10, 2008, SEC File No. 001-32567).10.28
    
    First Amendment to Loan and Security Agreement, dated as of December 18, 2008, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto
and Bank of America, N.A.10.29
    
    Credit Agreement, dated as of July 30, 2008, among Alon USA Energy, Inc., the financial
institutions from time to time a party thereto, Israel Discount Bank and Bank Leumi USA
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on August 1,
2008, SEC File No. 001-32567).10.30
    
    Management and Consulting Agreement, dated as of August 1, 2003, among Alon USA, Inc., Alon
Israel Oil Company, Ltd. and Alon USA Energy, Inc. (incorporated by reference to Exhibit
10.21 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.31
    
    Amendment, dated as of June 17, 2005, to the Management and Consulting Agreement, dated as
of August 1, 2003, among Alon USA, Inc., Alon Israel Oil Company, Ltd. and Alon USA Energy,
Inc. (incorporated by reference to Exhibit 10.21.1 to Form S-1/A, filed by the Company on
June 17, 2005, SEC File No. 333-124797).10.32
    
    Registration Rights Agreement, dated as of July 6, 2005, between Alon USA Energy, Inc. and
Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.22 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.33*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Jeff D. Morris and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.23 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.34*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA GP, LLC (incorporated by reference to Exhibit 10.9 to Form 10-Q,
filed by the Company on November 7, 2008, SEC File No. 001-32567).10.35*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Claire A. Hart and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.24 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.36*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Claire A. Hart and Alon USA GP, LLC (incorporated by reference to Exhibit 10.10 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.37*
    
    Executive Employment Agreement, dated as of February 5, 2001, between Joseph A. Concienne,
III and Alon USA GP, Inc., as amended by the Amendment to Executive/Management Employment
Agreement, dated May 1, 2005 (incorporated by reference to Exhibit 10.25 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.38*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Joseph A. Concienne, III and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.11
to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.39*
    
    Amended and Restated Management Employment Agreement, dated as of August 9, 2006, between
Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on August 10, 2006, SEC File No. 001-32567).10.40*
    
    Amendment to Amended and Restated Management Employment Agreement, dated as of November 4,
2008, between Harlin R. Dean and Alon USA GP, LLC. (incorporated by reference to Exhibit
10.12 to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.41*
    
    Management Employment Agreement, dated as of September 1, 2000, between Yosef Israel and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.33 to Form 10-K, filed by the
Company on March 15, 2006, SEC File No. 001-32567).10.42*
    
    Amendment to Executive/Management Employment Agreement, dated as of May 1, 2005 between
Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.34 to Form 10-K,
filed by the Company on March 15, 2006, SEC File No. 001-32567).10.43*
    
    Second Amendment to Executive/Management Employment Agreement, dated as of November 4, 2008,
between Yosef Israel and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.13 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.44*
    
    Executive Employment Agreement, dated as of August 1, 2003, between Shai Even and Alon USA
GP, LLC (incorporated by reference to Exhibit 10.49 to Form 10-K, filed by the Company on
March 15, 2007, SEC File No. 001-32567).10.45*
    
    Amendment to Executive Employment Agreement, dated as of November 4, 2008, between Shai Even
and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.14 to Form 10-Q, filed by the
Company on November 7, 2008, SEC File No. 001-32567).10.46*
    
    Annual Cash Bonus Plan (incorporated by reference to Exhibit 10.27 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.47*
    
    Description of 10% Bonus Plan (incorporated by reference to Exhibit 10.28 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.48*
    
    Description of Annual Bonus Plans (incorporated by reference to Exhibit 10.2 to Form 10-Q,
filed by the Company on June 6,, 2008, SEC File No. 001-32567).10.49*
    
    Change of Control Incentive Bonus Program (incorporated by reference to Exhibit 10.29 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.50*
    
    Description of Director Compensation (incorporated by reference to Exhibit 10.30 to Form
S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.51*
    
    Form of Director Indemnification Agreement (incorporated by reference to Exhibit 10.31 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.52*
    
    Form of Officer Indemnification Agreement (incorporated by reference to Exhibit 10.32 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.53*
    
    Form of Director and Officer Indemnification Agreement (incorporated by reference to Exhibit
10.33 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.54*
    
    Alon Assets, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.36 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.55*
    
    Alon USA Operating, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.37
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.56*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 (incorporated by reference to Exhibit 10.38 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.57 *
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon Assets, Inc. (incorporated by reference to Exhibit 10.15 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.58
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Jeff D.
Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.39 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.59*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 (incorporated by reference to Exhibit 10.40 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.60*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA Operating, Inc. (incorporated by reference to Exhibit 10.16 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.61
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and Jeff
D. Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.41 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.62*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Claire A. Hart, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.42 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.63
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Claire A.
Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.43 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.64*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Claire A. Hart, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.44
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.65
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and
Claire A. Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30,
2002 (incorporated by reference to Exhibit 10.45 to Form S-1/A, filed by the Company on June
17, 2005, SEC File No. 333-124797).10.66*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon Assets, Inc.
and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.46 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.67
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon Assets, Inc. and Joseph A.
Concienne, III (incorporated by reference to Exhibit 10.47 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.68*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon USA Operating,
Inc. and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.48 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.69
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon USA Operating, Inc. and
Joseph A. Concienne, III (incorporated by reference to Exhibit 10.49 to Form S-1/A, filed by
the Company on June 17, 2005, SEC File No. 333-124797).10.70*
    
    Agreement of Principles of Employment, dated as of July 6, 2005, between David Wiessman and
Alon USA Energy, Inc. (incorporated by reference to Exhibit 10.50 to Form S-1/A, filed by
the Company on July 7, 2005, SEC File No. 333-124797).10.71*
    
    Management Employment Agreement, dated as of October 30, 2008, between Michael Oster and
Alon USA GP,LLC.10.72*
    
    Alon USA Energy, Inc. 2005 Incentive Compensation Plan, as amended on November 7, 2005
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on November 8,
2005, SEC File No. 001-32567).10.73*
    
    Agreement, dated as of July 6, 2005, among Alon USA Energy, Inc., Alon USA, Inc., Alon USA
Capital, Inc., Alon USA Operating, Inc., Alon Assets, Inc., Jeff D. Morris, Claire A. Hart
and Joseph A. Concienne, III (incorporated by reference to Exhibit 10.52 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.74*
    
    Form of Restricted Stock Award Agreement relating to Director Grants pursuant to Section 12
of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on August 5, 2005, SEC File No. 001-32567).10.75*
    
    Form of Restricted Stock Award Agreement relating to Participant Grants pursuant to Section
8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference
to Exhibit 10.1 to Form 8-K, filed by the Company on August 23, 2005, SEC File No.
001-32567).10.76*
    
    Form II of Restricted Stock Award Agreement relating to Participant Grants pursuant to
Section 8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.3 to Form 8-K, filed by the Company on November 8, 2005, SEC File
No. 001-32567).10.77*
    
    Form of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on March 12, 2007, SEC File No.
001-32567).10.78
    
    Purchase and Sale Agreements, dated as of February 13, 2006, between Alon Petroleum Pipe
Line, LP and Sunoco Pipelines, LP, (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on February 13, 2006, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.79
    
    Stock Purchase Agreement, dated as of April 28, 2006, among Alon USA Energy, Inc., The Craig
C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The Jerrel C. Barto and
Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy, III and Mark R. Milano
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on May 2, 2006,
SEC File No. 001-32567).10.80
    
    First Amendment to Stock Purchase Agreement, dated as of June 30, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.1 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.81
    
    Second Amendment to Stock Purchase Agreement, dated as of July 31, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.2 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.82
    
    Agreement and Plan of Merger, dated as of April 28, 2006, among Alon USA Energy, Inc., Apex
Oil Company, Inc., Edgington Oil Company, and EOC Acquisition, LLC (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on May 2, 2006, SEC File No.
001-32567).10.83
    
    Agreement and Plan of Merger, dated March 2, 2007, by and among Alon USA Energy, Inc., Alon
USA Interests, LLC, ALOSKI, LLC, Skinnys, Inc. and the Davis Shareholders (as defined
therein) (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
March 6, 2007, SEC File No. 001-32567).10.84
    
    Stock Purchase Agreement, dated May 7, 2008, between Valero Refining and Marketing Company
and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.1 to Form
8-K, filed by the Company on May 13, 2008, SEC File No. 001-32567).10.85
    
    First Amendment to Stock Purchase Agreement, dated as of July 3, 2008, by and among Valero
Refining and Marketing Company, Alon Refining Krotz Springs, Inc. and Valero Refining
Company-Louisiana (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on July 10, 2008, SEC File No. 001-32567).10.86
    
    Series A Preferred Stock Purchase Agreement, dated as of July 3, 2008, by and between Alon
Refining Louisiana, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to
Exhibit 10.5 to Form 8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.87
    
    Stockholders Agreement, dated as of July 3, 2008, by and among Alon USA Energy, Inc., Alon
Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.
(incorporated by reference to Exhibit 10.6 to Form 8-K, filed by the Company on July 10,
2008, SEC File No. 001-32567).10.88
    
    Amended and Restated Stockholders Agreement dated as of March 31, 2009, by and among Alon USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.10.89
    
    Offtake Agreement, dated as of July 3, 2008, by and between Valero Marketing and Supply
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.9 to
Form 10-Q, filed by the Company on August 7, 2008, SEC File No. 001-32567).10.90
    
    Earnout Agreement, dated as of July 3, 2008, by and between Valero Refining and Marketing
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.10 to
Form 10-Q, filed by the Company on August 7, 2008, SEC File No. 001-32567).21.1
    
    Subsidiaries of Alon USA Energy, Inc.23.1
    
    Consent of KPMG LLP.31.1
    
    Certifications of Chief Executive Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certifications of Chief Financial Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.




---



##### 



Exhibit No.
    
    Description of Exhibit32.1
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
§1350, as adopted pursuant to §906 of the Sarbanes-Oxley Act of 2002.
 
 *
    
    Identifies management contracts and compensatory plans or arrangements.
    
    Filed under confidential treatment request.




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 INDEX TO CONSOLIDATED FINANCIAL STATEMENTS AND SCHEDULE
 PageAudited Consolidated Financial Statements:Report of Independent Registered Public Accounting Firm
    
    
    F-2Consolidated Balance Sheets as of December 31, 2008 and 2007
    
    
    F-4Consolidated Statements of Operations for the Years Ended December 31, 2008, 2007 and 2006
    
    
    F-5Consolidated Statements of Stockholders Equity for the Years Ended December 31, 2008, 2007 and 2006
    
    
    F-6Consolidated Statements of Cash Flows for the Years Ended December 31, 2008, 2007 and 2006
    
    
    F-7Notes to Consolidated Financial Statements
    
    
    F-8
 F-1




---



##### 



REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
 
    Fair Value
Measurements Accounting for Uncertainty in Income Taxes,
an interpretation of FASB Statement No. 109
 Internal ControlIntegrated Framework
  
 F-2




---



##### 



REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
 
 Internal ControlIntegrated Framework Managements Report on Internal Control over Financial Reporting
    Internal
ControlIntegrated Framework
    
 F-3




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 
 CONSOLIDATED BALANCE SHEETS
(in thousands except share data)
 As of December 31,2008
    
    
    2007ASSETSCurrent assets:Cash and cash equivalents
    
    $
    18,454
    
    
    $
    68,615Short-term investments
    
    
    
    
    
    
    27,296Accounts and other receivables, net
    
    
    204,576
    
    
    
    228,987Income tax receivable
    
    
    116,564
    
    
    
    35,244Inventories
    
    
    232,320
    
    
    
    300,689Prepaid expenses and other current assets
    
    
    81,758
    
    
    
    12,231Total current assets
    
    
    653,672
    
    
    
    673,062Equity method investments
    
    
    37,661
    
    
    
    40,092Property, plant, and equipment, net
    
    
    1,448,959
    
    
    
    713,592Goodwill
    
    
    105,943
    
    
    
    105,943Other assets
    
    
    167,198
    
    
    
    48,697Total assets
    
    $
    2,413,433
    
    
    $
    1,581,386LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable
    
    $
    233,004
    
    
    $
    291,339Accrued liabilities
    
    
    111,317
    
    
    
    75,980Current portion of deferred gain on disposition of assets
    
    
    
    
    
    
    8,805Current portion of long-term debt
    
    
    28,397
    
    
    
    11,154Deferred income tax liability
    
    
    30,570
    
    
    
    6,204Total current liabilities
    
    
    403,288
    
    
    
    393,482Other non-current liabilities
    
    
    104,190
    
    
    
    58,637Deferred gain on disposition of assets
    
    
    
    
    
    
    33,832Long-term debt
    
    
    1,075,172
    
    
    
    525,461Deferred income tax liability
    
    
    293,916
    
    
    
    166,052Total liabilities
    
    
    1,876,566
    
    
    
    1,177,464Commitments and contingencies (Note 21)Minority interest in subsidiaries
    
    
    20,648
    
    
    
    16,155Preferred stock of subsidiary including accumulated dividends
    
    
    84,300
    
    
    
    Stockholders equity:Preferred stock, par value $0.01, 10,000,000 shares
authorized; no shares issued and outstanding
    
    
    
    
    
    
    Common stock, par value $0.01, 100,000,000 shares
authorized; 46,814,021 and 46,808,444 shares issued and
outstanding at December 31, 2008 and 2007, respectively
    
    
    468
    
    
    
    468Additional paid-in capital
    
    
    183,642
    
    
    
    182,932Accumulated other comprehensive loss, net of income tax
    
    
    (40,086
    )
    
    
    (8,135
    )Retained earnings
    
    
    287,895
    
    
    
    212,502Total stockholders equity
    
    
    431,919
    
    
    
    387,767Total liabilities and stockholders equity
    
    $
    2,413,433
    
    
    $
    1,581,386
  F-4




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 
 CONSOLIDATED STATEMENTS OF OPERATIONS
(in thousands except per share data)
 Year Ended December 31,2008
    
    
    2007
    
    
    2006Net sales (1)
    
    $
    5,156,706
    
    
    $
    4,542,151
    
    
    $
    3,093,890Operating costs and expenses:Cost of sales
    
    
    4,853,195
    
    
    
    3,999,287
    
    
    
    2,627,321Direct operating expenses
    
    
    216,498
    
    
    
    201,196
    
    
    
    129,277Selling, general and administrative expenses
    
    
    119,852
    
    
    
    105,352
    
    
    
    86,939Net costs associated with fire
    
    
    56,854
    
    
    
    
    
    
    
    Business interruption recovery
    
    
    (55,000
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    66,754
    
    
    
    57,403
    
    
    
    34,274Total operating costs and expenses
    
    
    5,258,153
    
    
    
    4,363,238
    
    
    
    2,877,811Gain on involuntary conversion of assets
    
    
    279,680
    
    
    
    
    
    
    
    Gain on disposition of assets
    
    
    45,244
    
    
    
    7,206
    
    
    
    63,255Operating income
    
    
    223,477
    
    
    
    186,119
    
    
    
    279,334Interest expense
    
    
    (67,550
    )
    
    
    (47,747
    )
    
    
    (30,658
    )Equity earnings (loss) of investees
    
    
    (1,522
    )
    
    
    11,177
    
    
    
    3,161Other income, net
    
    
    1,500
    
    
    
    6,565
    
    
    
    7,740Income before income tax expense, minority interest in
income of subsidiaries, and accumulated dividends on
preferred stock of subsidiary
    
    
    155,905
    
    
    
    156,114
    
    
    
    259,577Income tax expense
    
    
    62,781
    
    
    
    46,199
    
    
    
    93,968Income before minority interest in income of subsidiaries
and accumulated dividends on preferred stock of subsidiary
    
    
    93,124
    
    
    
    109,915
    
    
    
    165,609Minority interest in income of subsidiaries
    
    
    5,941
    
    
    
    5,979
    
    
    
    8,241Accumulated dividends on preferred stock of subsidiary
    
    
    4,300
    
    
    
    
    
    
    
    Net income
    
    $
    82,883
    
    
    $
    103,936
    
    
    $
    157,368Earnings per share, basic
    
    $
    1.77
    
    
    $
    2.22
    
    
    $
    3.37Weighted average shares outstanding, basic (in thousands)
    
    
    46,788
    
    
    
    46,763
    
    
    
    46,738Earnings per share, diluted
    
    $
    1.72
    
    
    $
    2.16
    
    
    $
    3.36Weighted average shares outstanding, diluted (in thousands)
    
    
    49,583
    
    
    
    46,804
    
    
    
    46,779Cash dividends per share
    
    $
    0.16
    
    
    $
    0.16
    
    
    $
    3.03
 
 (1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $37,483,
$35,808, and $29,122 for the years ended December 31, 2008, 2007 and 2006, respectively.  F-5




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 
 CONSOLIDATED STATEMENTS OF STOCKHOLDERS EQUITY
(dollars in thousands)
 AccumulatedAdditional
    
    
    OtherCommon
    
    
    Paid-In
    
    
    Comprehensive
    
    
    RetainedStock
    
    
    Capital
    
    
    Income (Loss)
    
    
    Earnings
    
    
    TotalBalance at December 31, 2005
    
    $
    468
    
    
    $
    181,108
    
    
    $
    (2,596
    )
    
    $
    100,513
    
    
    $
    279,493Stock compensation expense
    
    
    
    
    
    
    514
    
    
    
    
    
    
    
    
    
    
    
    514Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (141,825
    )
    
    
    (141,825
    )Net income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    157,368
    
    
    
    157,368Other comprehensive loss:Minimum pension liability, net of income tax of $315
    
    
    
    
    
    
    
    
    
    
    (558
    )
    
    
    
    
    
    
    (558
    )Total comprehensive income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    156,810Adjustment to initially apply FASB Statement No. 158,
net of tax of $2,631
    
    
    
    
    
    
    
    
    
    
    (4,662
    )
    
    
    
    
    
    
    (4,662
    )Balance at December 31, 2006
    
    
    468
    
    
    
    181,622
    
    
    
    (7,816
    )
    
    
    116,056
    
    
    
    290,330Stock compensation expense
    
    
    
    
    
    
    1,310
    
    
    
    
    
    
    
    
    
    
    
    1,310Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (7,490
    )
    
    
    (7,490
    )Net income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    103,936
    
    
    
    103,936Other comprehensive income (loss):Defined benefit pension plans, net of income tax of
$958
    
    
    
    
    
    
    
    
    
    
    1,631
    
    
    
    
    
    
    
    1,631Fair value of interest rate swap, net of tax of $1,050
    
    
    
    
    
    
    
    
    
    
    (1,950
    )
    
    
    
    
    
    
    (1,950
    )Total comprehensive income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    103,617Balance at December 31, 2007
    
    
    468
    
    
    
    182,932
    
    
    
    (8,135
    )
    
    
    212,502
    
    
    
    387,767Stock compensation expense
    
    
    
    
    
    
    710
    
    
    
    
    
    
    
    
    
    
    
    710Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (7,490
    )
    
    
    (7,490
    )Net income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    82,883
    
    
    
    82,883Other comprehensive income (loss):Defined benefit pension plans, net of income tax of
$8,780
    
    
    
    
    
    
    
    
    
    
    (14,525
    )
    
    
    
    
    
    
    (14,525
    )Fair value of commodity derivative contracts, net of
tax of $677
    
    
    
    
    
    
    
    
    
    
    (1,154
    )
    
    
    
    
    
    
    (1,154
    )Fair value of interest rate swap, net of tax of $6,828
    
    
    
    
    
    
    
    
    
    
    (16,272
    )
    
    
    
    
    
    
    (16,272
    )Total comprehensive income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    50,932Balance at December 31, 2008
    
    $
    468
    
    
    $
    183,642
    
    
    $
    (40,086
    )
    
    $
    287,895
    
    
    $
    431,919
  F-6




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 
 CONSOLIDATED STATEMENTS OF CASH FLOWS
(dollars in thousands)
 Year Ended December 31,2008
    
    
    2007
    
    
    2006Cash flows from operating activities:Net income
    
    $
    82,883
    
    
    $
    103,936
    
    
    $
    157,368Adjustments to reconcile net income to cash provided by (used in)
operating activities:Depreciation and amortization
    
    
    66,754
    
    
    
    57,403
    
    
    
    34,274Stock compensation
    
    
    173
    
    
    
    2,264
    
    
    
    2,445Deferred income tax expense
    
    
    177,797
    
    
    
    (2,984
    )
    
    
    8,264Minority interest in income of subsidiaries
    
    
    10,241
    
    
    
    5,979
    
    
    
    8,241Equity earnings (loss) of investees (net of dividends)
    
    
    4,296
    
    
    
    (1,876
    )
    
    
    (739
    )Mark-to-market of heating oil hedge
    
    
    (117,452
    )
    
    
    
    
    
    
    Gain on involuntary conversion of assets
    
    
    (279,680
    )
    
    
    
    
    
    
    Gain on disposition of assets
    
    
    (45,244
    )
    
    
    (7,206
    )
    
    
    (63,255
    )Changes in operating assets and liabilities, net of acquisition effects:Accounts and other receivables, net
    
    
    59,336
    
    
    
    (144,068
    )
    
    
    68,900Income tax receivable
    
    
    (81,320
    )
    
    
    
    
    
    
    Inventories
    
    
    213,373
    
    
    
    16,715
    
    
    
    (20,490
    )Prepaid expenses and other current assets
    
    
    5,933
    
    
    
    794
    
    
    
    9,639Other assets
    
    
    (1,136
    )
    
    
    9,654
    
    
    
    26,217Accounts payable
    
    
    (108,458
    )
    
    
    82,141
    
    
    
    (88,664
    )Accrued liabilities
    
    
    17,419
    
    
    
    8,312
    
    
    
    (13,787
    )Other non-current liabilities
    
    
    (5,727
    )
    
    
    (7,114
    )
    
    
    14,564Net cash provided by (used in) operating activities
    
    
    (812
    )
    
    
    123,950
    
    
    
    142,977Cash flows from investing activities:Capital expenditures
    
    
    (62,356
    )
    
    
    (42,204
    )
    
    
    (39,832
    )Capital expenditures to rebuild the Big Spring refinery
    
    
    (362,178
    )
    
    
    
    
    
    
    Capital expenditures for turnarounds and catalysts
    
    
    (9,958
    )
    
    
    (9,842
    )
    
    
    (3,940
    )Proceeds from insurance to rebuild the Big Spring refinery
    
    
    270,885
    
    
    
    
    
    
    
    Proceeds from disposition of assets
    
    
    7,000
    
    
    
    
    
    
    
    68,009Sale (purchase) of short-term investments, net
    
    
    27,296
    
    
    
    (27,296
    )
    
    
    185,320Acquisition of Krotz Springs refinery
    
    
    (481,011
    )
    
    
    
    
    
    
    Acquisition of Skinnys, Inc. stock
    
    
    
    
    
    
    (75,329
    )
    
    
    Acquisition of Good Time stores assets
    
    
    
    
    
    
    
    
    
    
    (27,024
    )Acquisition of Paramount Petroleum Corporation stock
    
    
    
    
    
    
    7,417
    
    
    
    (504,655
    )Acquisition of Edgington Oil Company assets
    
    
    
    
    
    
    
    
    
    
    (98,762
    )Minority interest shares purchased
    
    
    
    
    
    
    
    
    
    
    (186
    )Net cash used in investing activities
    
    
    (610,322
    )
    
    
    (147,254
    )
    
    
    (421,070
    )Cash flows from financing activities:Dividends paid to minority interest shareholders
    
    
    (386
    )
    
    
    (468
    )
    
    
    (7,968
    )Dividends paid to shareholders
    
    
    (7,490
    )
    
    
    (7,490
    )
    
    
    (141,825
    )Proceeds from sale of preferred stock by subsidiary
    
    
    80,000
    
    
    
    
    
    
    
    Deferred debt issuance costs
    
    
    (28,105
    )
    
    
    (2,235
    )
    
    
    (11,047
    )Revolving credit facilities, net
    
    
    276,818
    
    
    
    
    
    
    
    19,798Additions to long-term debt
    
    
    252,000
    
    
    
    46,334
    
    
    
    500,000Payments on long-term debt
    
    
    (11,864
    )
    
    
    (8,388
    )
    
    
    (153,519
    )Net cash provided by financing activities
    
    
    560,973
    
    
    
    27,753
    
    
    
    205,439Net increase (decrease) in cash and cash equivalents
    
    
    (50,161
    )
    
    
    4,449
    
    
    
    (72,654
    )Cash and cash equivalents, beginning of period
    
    
    68,615
    
    
    
    64,166
    
    
    
    136,820Cash and cash equivalents, end of period
    
    $
    18,454
    
    
    $
    68,615
    
    
    $
    64,166Supplemental cash flow information:Cash paid for interest, net of capitalized interest
    
    $
    58,504
    
    
    $
    48,686
    
    
    $
    20,301Cash (received) paid for income tax, net of refunds
    
    $
    (30,334
    )
    
    $
    91,781
    
    
    $
    83,291Non-cash activities:Financing activity  proceeds from borrowings retained by bank as deposit
for hedge related activities for Krotz Springs refinery acquisition
    
    $
    50,000
    
    
    $
    
    
    
    $
    
  F-7




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (1) Description and Nature of Business
   Refining and Unbranded Marketing Segment
    Asphalt Segment
  Retail and Branded Marketing Segment
 F-8




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (2) Summary of Significant Accounting Policies
 (a) Basis of Presentation
  (b) Use of Estimates
  (c) Revenue Recognition
     (d) Cost Classifications
  F-9




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    (e) Cash and Cash Equivalents
  (f) Short-Term Investments
  (g) Accounts Receivable
  (h) Inventories
  (i) Hedging Activity
  F-10




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   (j) HEP Investment
  (k) Property, Plant, and Equipment
     (l) Impairment of Long-Lived Assets and Assets To Be Disposed Of
  (m) Asset Retirement Obligations
 Accounting for Asset
Retirement Obligations
 F-11




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 Accounting for Conditional Retirement Obligations
 (n) Turnarounds and Chemical Catalyst Costs
  (o) Income Taxes
 Accounting for Income Taxes, Accounting for Uncertainty in Income
Taxes
 (p) Stock-Based Compensation
 Share-Based Payment Accounting for Stock-Based Compensation
 Accounting for Stock Issued to
Employees
  (q) Environmental Expenditures
   F-12




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (r) Earnings Per Share
  (s) Other Comprehensive Income (Loss)
  (t) Defined Benefit Pension and Other Postretirement Plans
 Employers Accounting for Defined Benefit
Pension and Other Postretirement Plans Employers Accounting for
Pensions Employers Accounting for Settlements and Curtailments of Defined Benefit
Pension Plans and for Termination Benefits, Employers Accounting for
Postretirement Benefits Other Than Pensions Employers Disclosures
about Pensions and Other Postretirement Benefits
   Before Application
    
    
    
    
    
    After Applicationof Statement 158
    
    Adjustments
    
    of Statement 158Accrued benefit liability
    
    $
    6,732
    
    
    $
    7,318
    
    
    $
    14,050Deferred income taxes
    
    
    1,897
    
    
    
    2,631
    
    
    
    4,528Accumulated other comprehensive income
    
    
    3,154
    
    
    
    4,662
    
    
    
    7,816
 (u) Commitments and Contingencies
 Offsetting of Amounts Related to Certain Contracts
 (v) Goodwill and Intangible Assets
  F-13




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (w) New Accounting Standards and Disclosures
 Employers Disclosures about
Postretirement Benefit Plans Employers Disclosures about Pensions and Other Postretirement Benefits
 Equity Method
Investment Accounting Considerations
 Accounting by Lessees
for Maintenance Deposits
 Determination of the Useful Life
of Intangible Assets Goodwill and Other
Intangible Assets.
 Disclosure about Derivative Instruments and
Hedging Activities
 Fair Value
Measurements
 F-14




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Partial Deferral of the
Effective Date of Statement 157
 The Fair Value Option for Financial Assets and
Financial Liabilities
 Non-controlling Interests in Consolidated
Financial Statements, an Amendment of ARB 51
 Business Combinations
 Accounting for Uncertainty in Income
Taxes, an interpretation of FASB Statement No. 109
 How Taxes Collected from
Customers and Remitted to Governmental Authorities Should Be Presented in the Income Statement
(That Is, Gross versus Net Presentation)
 F-15




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (x) Reclassifications
  (3) Big Spring Refinery Fire
      (4) Acquisition s
 Krotz Springs Refinery Acquisition
     F-16




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   Cash paid
    
    $
    474,494Transaction costs
    
    
    6,517Total purchase price
    
    $
    481,011
  Current assets
    
    $
    145,859Property, plant and equipment
    
    
    341,702Current liabilities
    
    
    (5,309
    )Other non-current liabilities
    
    
    (1,241
    )Total purchase price
    
    $
    481,011
   Unaudited Pro Forma Financial Information
  
    
    The acquisition of the Krotz Springs refining business occurred on January 1, 2007;
    
    $302,000 of term debt and $141,494 of borrowings under the revolver was incurred on
January 1, 2007 to fund the acquisition and buy initial inventories; and
    
    Depreciation expense was higher beginning January 1, 2007 based upon the revaluation of
estimated asset values as of that date.
 F-17




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 Year EndedDecember 31,2008
    
    
    2007(pro forma)
    
    
    (pro forma)Net sales
    
    $
    6,696,335
    
    
    $
    6,835,637Operating income
    
    
    167,971
    
    
    
    229,580Net income
    
    
    31,553
    
    
    
    97,271Earnings per share, basic
    
    $
    0.67
    
    
    $
    2.08
 Skinnys Acquisition
    Cash paid, net of unrestricted cash acquired
    
    $
    74,787Transaction costs
    
    
    542Total purchase price
    
    $
    75,329
  Current assets, net of unrestricted cash acquired
    
    $
    7,002Property, plant and equipment
    
    
    43,684Other assets
    
    
    771Goodwill
    
    
    34,471Intangibles
    
    
    827Current liabilities
    
    
    (10,483
    )Other non-current liabilities
    
    
    (943
    )Total purchase price
    
    $
    75,329
  Pipeline Acquisition
  (5) Contribution and Sale of Pipelines and Terminals
 HEP Transaction
  F-18




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    Amdel and White Oil Transaction
 (6) Segment Data
  (a) Refining and Unbranded Marketing Segment
  (b) Asphalt Segment
  F-19




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (c) Retail and Branded Marketing Segment
  (d) Corporate
   Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2008
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    3,282,166
    
    
    $
    647,221
    
    
    $
    1,227,319
    
    
    $
    
    
    
    $
    5,156,706Intersegment sales/purchases
    
    
    623,332
    
    
    
    (369,505
    )
    
    
    (253,827
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    50,047
    
    
    
    2,139
    
    
    
    13,674
    
    
    
    894
    
    
    
    66,754Operating income (loss)
    
    
    128,772
    
    
    
    97,442
    
    
    
    (1,239
    )
    
    
    (1,498
    )
    
    
    223,477Total assets
    
    
    1,973,324
    
    
    
    231,921
    
    
    
    193,815
    
    
    
    14,373
    
    
    
    2,413,433Capital expenditures to
rebuild the Big Spring
refinery
    
    
    362,178
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    362,178Turnaround, chemical catalyst
and capital expenditures
    
    
    67,534
    
    
    
    644
    
    
    
    2,928
    
    
    
    1,208
    
    
    
    72,314
 Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2007
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    2,624,698
    
    
    $
    642,937
    
    
    $
    1,274,516
    
    
    $
    
    
    
    $
    4,542,151Intersegment sales/purchases
    
    
    700,392
    
    
    
    (502,924
    )
    
    
    (197,468
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    44,107
    
    
    
    2,145
    
    
    
    10,245
    
    
    
    906
    
    
    
    57,403Operating income (loss)
    
    
    165,073
    
    
    
    (1,671
    )
    
    
    24,146
    
    
    
    (1,429
    )
    
    
    186,119Total assets
    
    
    1,086,020
    
    
    
    238,423
    
    
    
    237,015
    
    
    
    19,928
    
    
    
    1,581,386Turnaround, chemical catalyst
and capital expenditures
    
    
    38,511
    
    
    
    2,167
    
    
    
    9,797
    
    
    
    1,571
    
    
    
    52,046
 Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2006
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    1,439,663
    
    
    $
    389,634
    
    
    $
    1,264,593
    
    
    $
    
    
    
    $
    3,093,890Intersegment sales/purchases
    
    
    387,840
    
    
    
    (245,434
    )
    
    
    (142,406
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    24,209
    
    
    
    2,247
    
    
    
    6,205
    
    
    
    1,613
    
    
    
    34,274Operating income (loss)
    
    
    261,116
    
    
    
    11,171
    
    
    
    9,171
    
    
    
    (2,124
    )
    
    
    279,334Total assets
    
    
    1,112,142
    
    
    
    144,871
    
    
    
    141,465
    
    
    
    10,307
    
    
    
    1,408,785Turnaround, chemical catalyst
and capital expenditures
    
    
    30,479
    
    
    
    3,156
    
    
    
    9,949
    
    
    
    188
    
    
    
    43,772
 F-20




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   (7) Fair Value
    Quoted PricesinActive Markets
    
    Significantfor Identical
    
    Other
    
    SignificantAssets or
    
    Observable
    
    UnobservableLiabilities
    
    Inputs
    
    Inputs
    
    ConsolidatedYear ended December 31, 2008
    
    (Level 1)
    
    (Level 2)
    
    (Level 3)
    
    TotalAssets:Commodity swaps
    
    $
    
    
    
    $
    117,485
    
    
    $
    
    
    
    $
    117,485Liabilities:Futures and forwards
    
    
    1,197
    
    
    
    
    
    
    
    
    
    
    
    1,197Commodity swaps
    
    
    
    
    
    
    25,473
    
    
    
    
    
    
    
    25,473Interest rate swaps
    
    
    
    
    
    
    26,100
    
    
    
    
    
    
    
    26,100Year ended December 31, 2007LiabilitiesFutures and forwards
    
    
    4,250
    
    
    
    
    
    
    
    
    
    
    
    4,250Interest rate swaps
    
    
    
    
    
    
    3,000
    
    
    
    
    
    
    
    3,000
 (8) Derivative Instruments
 Commodity Derivatives  Mark to Market
  F-21




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
       Cash Flow Hedges
  Interest Rate Derivatives.
  F-22




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Commodity Derivatives.
  (9) Accounts and Other Receivables
   December 31,2008
    
    
    2007Trade accounts receivable
    
    $
    172,513
    
    
    $
    219,978Insurance receivable
    
    
    34,125
    
    
    
    Other receivables
    
    
    18,782
    
    
    
    10,602Total accounts and other receivables
    
    $
    225,420
    
    
    $
    230,580
   Balance at
    
    AdditionsBeginning of
    
    Charged to
    
    
    
    
    
    Balance at EndPeriod
    
    Expense
    
    Deductions (1)
    

of Period(amounts in thousands)Allowance for doubtful accounts:2008
    
    $
    1,593
    
    
    
    20,122
    
    
    
    (871
    )
    
    $
    20,8442007
    
    $
    1,251
    
    
    
    161
    
    
    
    181
    
    
    $
    1,5932006
    
    $
    1,145
    
    
    
    
    
    
    
    106
    
    
    $
    1,251
 
 (1)
    
    Amounts written off net of recoveries. F-23




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 SEMGroup, LP Bankruptcy
  (10) Inventories
   December 31,2008
    
    
    2007Crude oil, refined products, asphalt and blendstocks
    
    $
    192,997
    
    
    $
    261,816Materials and supplies
    
    
    16,456
    
    
    
    12,789Store merchandise
    
    
    19,875
    
    
    
    18,197Store fuel
    
    
    2,992
    
    
    
    7,887Total inventories
    
    $
    232,320
    
    
    $
    300,689
   (11) Property, Plant, and Equipment, Net
  December 31,2008
    
    
    2007Refining facilities
    
    $
    1,430,896
    
    
    $
    645,653Pipelines and terminals
    
    
    39,161
    
    
    
    45,158Retail
    
    
    134,263
    
    
    
    131,556Other
    
    
    13,052
    
    
    
    12,271Property, plant and equipment, gross
    
    
    1,617,372
    
    
    
    834,638Less accumulated depreciation
    
    
    (168,413
    )
    
    
    (121,046
    )Property, plant and equipment, net
    
    $
    1,448,959
    
    
    $
    713,592
 F-24




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Refining facilities
    
    3 - 20 years; average 18 yearsPipelines and terminals
    
    5 - 25 years; average 23 yearsRetail
    
    5 - 40 years; average 8 yearsOther
    
    3 - 15 years; average 5 years
   (12) Other Assets
  December 31,2008
    
    
    2007Deferred turnaround and chemical catalyst cost
    
    $
    11,684
    
    
    $
    9,232Environmental receivables
    
    
    8,524
    
    
    
    9,425Deferred debt issuance costs
    
    
    35,648
    
    
    
    11,286Intangible assets
    
    
    7,055
    
    
    
    7,488Deposit for hedge related activities for Krotz Springs refinery acquisition
    
    
    50,000
    
    
    
    Commodity swaps
    
    
    42,080
    
    
    
    Other
    
    
    12,207
    
    
    
    11,266Total other assets
    
    $
    167,198
    
    
    $
    48,697
   F-25




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (13) Accrued Liabilities and Other Non-Current Liabilities
  December 31,2008
    
    
    2007Accrued Liabilities:Taxes other than income taxes, primarily excise taxes
    
    $
    27,789
    
    
    $
    21,026Employee costs
    
    
    4,884
    
    
    
    6,853Commodity Swaps
    
    
    26,670
    
    
    
    Other
    
    
    51,974
    
    
    
    48,101Total accrued liabilities
    
    $
    111,317
    
    
    $
    75,980Other Non-Current Liabilities:Pension and other postemployment benefit liabilities, net (Note 14)
    
    $
    35,989
    
    
    $
    14,137Environmental accrual (Note 21)
    
    
    33,181
    
    
    
    34,992Asset retirement obligation
    
    
    8,386
    
    
    
    7,378Interest rate swap valuations
    
    
    26,100
    
    
    
    Other
    
    
    534
    
    
    
    2,130Total other non-current liabilities
    
    $
    104,190
    
    
    $
    58,637
    December 31,2008
    
    
    2007Balance at beginning of year
    
    $
    7,378
    
    
    $
    6,216Accretion expense
    
    
    342
    
    
    
    377Additional accretion due to change in risk free interest rate
    
    
    
    
    
    
    Retirements
    
    
    (150
    )
    
    
    (52
    )Additions
    
    
    816
    
    
    
    837Balance at end of year
    
    $
    8,386
    
    
    $
    7,378
  (14) Employee and Postretirement Benefits
 (a) Retirement Plans
  F-26




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Pension Benefits2008
    
    
    2007Change in projected benefit obligation:Benefit obligation at beginning of year
    
    $
    45,409
    
    
    $
    45,172Service cost
    
    
    2,307
    
    
    
    1,979Interest cost
    
    
    2,889
    
    
    
    2,568Plan participants contributions
    
    
    
    
    
    
    Plan amendments
    
    
    276
    
    
    
    Actuarial loss (gain)
    
    
    6,767
    
    
    
    (3,200
    )Benefits paid
    
    
    (1,435
    )
    
    
    (1,110
    )Projected benefit obligations at end of year
    
    $
    56,213
    
    
    $
    45,409Change in plan assets:Fair value of plan assets at beginning of year
    
    
    35,324
    
    
    
    31,122Actual (loss) gain on plan assets
    
    
    (13,380
    )
    
    
    1,317Employer contribution
    
    
    3,325
    
    
    
    3,995Plan participants contributions
    
    
    
    
    
    
    Benefits paid
    
    
    (1,435
    )
    
    
    (1,110
    )Fair value of plan assets at end of year
    
    $
    23,834
    
    
    $
    35,324Reconciliation of funded status:Fair value of plan assets at end of year
    
    $
    23,834
    
    
    $
    35,324Less projected benefit obligations at end of year
    
    
    56,213
    
    
    
    45,409Under-funded status at end of year
    
    $
    (32,379
    )
    
    $
    (10,085
    )
  Pension Benefits2008
    
    
    2007Amounts recognized in the consolidated balance sheets:Pension benefit liability
    
    $
    (32,379
    )
    
    $
    (10,085
    )
  Pension Benefits2008
    
    
    2007Net actuarial loss
    
    $
    (33,563
    )
    
    $
    (10,612
    )Prior service credit
    
    
    603
    
    
    
    957Total
    
    $
    (32,960
    )
    
    $
    (9,655
    )
  PensionBenefitsAmortization of prior service cost (credit)
    
    $
    (58
    )Amortization of loss
    
    
    1,109Total
    
    $
    1,051
 F-27




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  December 31,2008
    
    2007Projected benefit obligation
    
    $
    56,213
    
    
    $
    45,409Accumulated benefit obligation
    
    
    48,460
    
    
    
    40,346Fair value of plan assets
    
    
    23,834
    
    
    
    35,324
  Pension Benefits2008
    
    2007
    
    2006Discount rate
    
    
    6.07
    %
    
    
    6.46
    %
    
    
    5.75
    %Rate of compensation increase
    
    
    3.50
    %
    
    
    3.50
    %
    
    
    3.50
    %
  Pension Benefits2008
    
    2007
    
    2006Discount rate
    
    
    6.46
    %
    
    
    5.75
    %
    
    
    6.00
    %Expected return on plan assets
    
    
    9.00
    %
    
    
    9.00
    %
    
    
    9.00
    %Rate of compensation increase
    
    
    3.50
    %
    
    
    3.50
    %
    
    
    3.50
    %
  Pension BenefitsYear Ended December 312008
    
    
    2007
    
    
    2006Components of net periodic benefit cost:Service cost
    
    $
    2,307
    
    
    $
    1,979
    
    
    $
    1,867Interest cost
    
    
    2,889
    
    
    
    2,568
    
    
    
    2,325Amortization of prior service costs
    
    
    (78
    )
    
    
    (41
    )
    
    
    63Expected return on plan assets
    
    
    (3,284
    )
    
    
    (2,809
    )
    
    
    (2,371
    )Recognized net actuarial loss
    
    
    481
    
    
    
    766
    
    
    
    573Net periodic benefit cost
    
    $
    2,315
    
    
    $
    2,463
    
    
    $
    2,457
 Plan Assets
  Pension BenefitsPlan Assets2008
    
    2007Asset Category:Equity securities
    
    
    74.0
    %
    
    
    77.0
    %Debt securities
    
    
    16.0
    %
    
    
    14.0
    %Real estate investment trust
    
    
    10.0
    %
    
    
    9.0
    %Total
    
    
    100.0
    %
    
    
    100.0
    %
  F-28




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Cash Flows
     (b) Postretirement Medical Plan
   (15) Long-Term Debt
  December 31,2008
    
    
    2007Term loan credit facilities
    
    $
    739,810
    
    
    $
    443,250Revolving credit facilities
    
    
    276,818
    
    
    
    Retail credit facilities
    
    
    86,941
    
    
    
    93,365Total debt
    
    
    1,103,569
    
    
    
    536,615Less current portion
    
    
    (28,397
    )
    
    
    (11,154
    )Total long-term debt
    
    $
    1,075,172
    
    
    $
    525,461
 (a) Alon USA Energy, Inc. Credit Facilities
 Term Loan Credit Facility
 F-29




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    Letters of Credit Facility.
 (b) Alon USA, LP Credit Facilities
 Revolving Credit Facility.
   (c) Paramount Petroleum Corporation Credit Facility
 Revolving Credit Facility.
 F-30




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   (d) Alon Refining Krotz Springs, Inc. Credit Facilities
 Term Loan Credit Facility
     Revolving Credit Facility.
     F-31




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   (e) Retail Credit Facilities
      (f) Other Retail Related Credit Facilities
   (g) Secured Term Loan
  F-32




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (h) Maturity of Long-Term Debt
  (i) Interest and Financing Expense
  December 31,2008
    
    
    2007
    
    
    2006Interest expense
    
    $
    56,706
    
    
    $
    39,559
    
    
    $
    17,685Letters of credit and finance charges
    
    
    10,133
    
    
    
    6,095
    
    
    
    6,333Amortization of debt issuance costs
(includes write off of unamortized debt
issuance cost in 2006 of $6,091)
    
    
    4,128
    
    
    
    2,093
    
    
    
    6,640Capitalized interest
    
    
    (3,417
    )
    
    
    
    
    
    
    Total interest expense
    
    $
    67,550
    
    
    $
    47,747
    
    
    $
    30,658
 16) Income Taxes
  December 31,2008
    
    
    2007
    
    
    2006Current:Federal
    
    $
    (117,679
    )
    
    $
    49,237
    
    
    $
    77,372State
    
    
    2,663
    
    
    
    (54
    )
    
    
    8,332Total current
    
    
    (115,016
    )
    
    
    49,183
    
    
    
    85,704Deferred:Federal
    
    
    170,869
    
    
    
    (2,762
    )
    
    
    5,035State
    
    
    6,928
    
    
    
    (222
    )
    
    
    3,229Total deferred
    
    
    177,797
    
    
    
    (2,984
    )
    
    
    8,264Income tax expense
    
    $
    62,781
    
    
    $
    46,199
    
    
    $
    93,968
  December 31,2008
    
    
    2007
    
    
    2006Computed expected tax expense
    
    $
    54,567
    
    
    $
    54,640
    
    
    $
    90,852State and local income taxes, net of federal benefit
    
    
    6,234
    
    
    
    (4,960
    )
    
    
    7,516Deduction for qualified production income
    
    
    4,343
    
    
    
    (3,403
    )
    
    
    (2,049
    )Low-sulfur diesel tax credit
    
    
    
    
    
    
    
    
    
    
    (2,918
    )Other, net
    
    
    (2,363
    )
    
    
    (78
    )
    
    
    567Income tax expense
    
    $
    62,781
    
    
    $
    46,199
    
    
    $
    93,968
 F-33




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   December 31,2008
    
    
    2007Deferred income tax assets:Accounts receivable, allowance
    
    $
    352
    
    
    $
    595Deferred gain
    
    
    
    
    
    
    3,640Intangibles
    
    
    
    
    
    
    1,140Accrued liabilities and other
    
    
    10,735
    
    
    
    3,941Post retirement benefits
    
    
    12,416
    
    
    
    3,418Non-current accrued liabilities and other
    
    
    4,125
    
    
    
    4,297Net operating loss carryover
    
    
    17,062
    
    
    
    6,101Tax credits
    
    
    1,583
    
    
    
    1,583Other
    
    
    736
    
    
    
    706Deferred income tax assets
    
    
    47,009
    
    
    
    25,421Deferred income tax liabilities:Deferred charges
    
    
    (1,938
    )
    
    
    (681
    )Unrealized Gains
    
    
    (54,556
    )
    
    
    Property, plant, and equipment
    
    
    (289,959
    )
    
    
    (156,722
    )Other non-current
    
    
    (9,957
    )
    
    
    (22,468
    )Inventories
    
    
    (15,085
    )
    
    
    (10,761
    )Deferred income tax liabilities
    
    $
    (371,495
    )
    
    $
    (190,632
    )
    F-34




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (17) Related-Party Transactions
 (a) Consulting Agreement
  (b) Sale of Preferred Shares
     (18) Stockholders Equity
 (a) Common and preferred stock
  F-35




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  CommonStock(in thousands)Balance as of December 31, 2006
    
    
    46,806Shares forfeited
    
    
    Shares issued in connection with stock plans (Note 20)
    
    
    2Balance as of December 31, 2007
    
    
    46,808Shares forfeited
    
    
    Shares issued in connection with stock plans (Note 20)
    
    
    6Balance as of December 31, 2008
    
    
    46,814
 (b) Dividends
     (19) Earnings per Share
  F-36




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  December 312008
    
    
    2007
    
    
    2006Net income
    
    $
    82,883
    
    
    $
    103,936
    
    
    $
    157,368Average number of shares of common stock outstanding
    
    
    46,788
    
    
    
    46,763
    
    
    
    46,738Dilutive restricted shares, SARs, and convertible preferred shares
    
    
    2,795
    
    
    
    41
    
    
    
    41Average number of shares of common stock outstanding assuming dilution
    
    
    49,583
    
    
    
    46,804
    
    
    
    46,779Earnings per share  basic
    
    $
    1.77
    
    
    $
    2.22
    
    
    $
    3.37Earnings per share  diluted *
    
    $
    1.72
    
    
    $
    2.16
    
    
    $
    3.36
 
 *
    
    For the purpose of calculating diluted earnings per share, net income was reduced to adjust
for the effects of options issued by Alons subsidiaries. The adjustment to net income for
options issued for the calculation of diluted earnings per share for December 31, 2008, 2007
and 2006 was $1,449, $2,391, and $191, respectively. Additionally, net income for the year
ended December 31, 2008 was adjusted $3,991 for preferred stock dividends that would no longer
be paid if the preferred stock was converted to shares of common stock. (20) Stock Based Compensation
  (a) 2005 Incentive Compensation Plan (share value in dollars)
  Restricted Stock
  Weighted AverageNonvested Shares
    
    Shares
    
    
    Grant Date Fair ValuesNonvested at January 1, 2008
    
    
    26,918
    
    
    $
    21.74Granted
    
    
    5,577
    
    
    
    13.45Vested
    
    
    (24,833
    )
    
    
    20.54Forfeited
    
    
    
    
    
    
    Nonvested at December 31, 2008
    
    
    7,662
    
    
    $
    19.58
 F-37




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Stock Appreciation Rights.
  (b) 2000 Incentive Stock Compensation Plan
   Alon Assets
    
    
    Alon OperatingWeighted
    
    
    
    
    
    
    WeightedNumber of
    
    
    Average
    
    
    Number of
    
    
    AverageOptions
    
    
    Exercise
    
    
    Options
    
    
    ExerciseOutstanding
    
    
    Price
    
    
    Outstanding
    
    
    PriceOutstanding at December 31, 2006
    
    
    6,848
    
    
    $
    100
    
    
    
    2,572
    
    
    $
    100Granted
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Exercised
    
    
    (1,632
    )
    
    
    100
    
    
    
    (613
    )
    
    
    100Forfeited and expired
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Outstanding at December 31, 2007
    
    
    5,216
    
    
    $
    100
    
    
    
    1,959
    
    
    $
    100Granted
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Exercised
    
    
    (2,423
    )
    
    
    100
    
    
    
    (910
    )
    
    
    100Forfeited and expired
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Outstanding at December 31, 2008
    
    
    2,793
    
    
    $
    100
    
    
    
    1,049
    
    
    $
    100
  F-38




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (21) Commitments and Contingencies
 (a) Leases
  Year ending December 31:2009
    
    $
    38,2362010
    
    
    32,0602011
    
    
    27,2882012
    
    
    25,7862013
    
    
    14,3402014 and thereafter
    
    
    76,392Total
    
    $
    214,102
  (b) Other Commitments
      F-39




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   (c) Environmental
      F-40




---



##### 



ALON USA ENERGY, INC. AND SUBSIDIARIES
 NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (22) Quarterly Information (unaudited)
  QuartersFirst
    
    Second
    
    Third
    
    Fourth
    
    Full Year2008Net sales
    
    $
    1,020,763
    
    
    $
    1,244,671
    
    
    $
    1,905,106
    
    
    $
    986,166
    
    
    $
    5,156,706Operating income (loss)
    
    
    (47,273
    )
    
    
    40,573
    
    
    
    92,505
    
    
    
    137,672
    
    
    
    223,477Net income (loss)
    
    
    (33,578
    )
    
    
    18,227
    
    
    
    37,297
    
    
    
    60,937
    
    
    
    82,883Earnings (loss) per share, basic
    
    $
    (0.72
    )
    
    $
    0.39
    
    
    $
    0.80
    
    
    $
    1.30
    
    
    $
    1.77Weighted average shares outstanding
    
    
    46,782
    
    
    
    46,782
    
    
    
    46,786
    
    
    
    46,800
    
    
    
    46,7882007Net sales
    
    $
    965,905
    
    
    $
    1,187,181
    
    
    $
    1,243,723
    
    
    $
    1,145,342
    
    
    $
    4,542,151Operating income (loss)
    
    
    69,336
    
    
    
    166,710
    
    
    
    16,990
    
    
    
    (66,917
    )
    
    
    186,119Net income (loss)
    
    
    35,565
    
    
    
    95,613
    
    
    
    12,627
    
    
    
    (39,869
    )
    
    
    103,936Earnings (loss) per share, basic
    
    $
    0.76
    
    
    $
    2.05
    
    
    $
    0.27
    
    
    $
    (0.85
    )
    
    $
    2.22Weighted average shares outstanding
    
    
    46,757
    
    
    
    46,758
    
    
    
    46,761
    
    
    
    46,775
    
    
    
    46,763
 (23) Subsequent Events
 Dividend Announcement
  F-41




---



##### 



SIGNATURES
  April 9, 2009
    By:
    /s/ Jeff D. MorrisJeff D. MorrisChief Executive Officer  April 9, 2009
    By:
    /s/ David WiessmanDavid WiessmanExecutive ChairmanApril 9, 2009
    By:
    /s/ Jeff D. MorrisJeff D. MorrisPresident, Chief Executive Officer and DirectorApril 9, 2009
    By:
    /s/ Shai EvenShai EvenSenior Vice President and Chief Financial OfficerApril 9, 2009
    By:
    /s/ Ron W. HaddockRon W. HaddockDirectorApril 9, 2009
    By:
    /s/ Itzhak BaderItzhak BaderDirectorApril 9, 2009
    By:
    /s/ Ron FainaroRon FainaroDirectorApril 9, 2009
    By:
    /s/ Avraham Baiga ShochatAvraham Baiga ShochatDirectorApril 9, 2009
    By:
    /s/ Yeshayahu PeryYeshayahu PeryDirectorApril 9, 2009
    By:
    /s/ Zalman SegalZalman SegalDirectorApril 9, 2009
    By:
    /s/ Boaz BiranBoaz BiranDirectorApril 9, 2009
    By:
    /s/ Avinadav GrinshponAvinadav GrinshponDirector




---



##### 



Exhibit No.
    
    Description of Exhibit3.1
    
    Amended and Restated Certificate of Incorporation of Alon USA Energy, Inc. (incorporated by
reference to Exhibit 3.1 to Form S-1/A, filed by the Company on July 7, 2005, SEC File No.
333-124797).3.2
    
    Amended and Restated Bylaws of Alon USA Energy, Inc. (incorporated by reference to Exhibit
3.2 to Form S-1/A, filed by the Company on July 14, 2005, SEC File No. 333-124797).4.1
    
    Specimen Common Stock Certificate (incorporated by reference to Exhibit 4.1 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.1
    
    Trademark License Agreement, dated as of July 31, 2000, among Finamark, Inc., Atofina
Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.3 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.2
    
    First Amendment to Trademark License Agreement, dated as of April 11, 2001, among Finamark,
Inc., Atofina Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.4
to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.3
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, L.P. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on February 2, 2008, SEC File No. 001-32567).10.4
    
    Pipeline Lease Agreement, dated as of February 21, 1997, between Navajo Pipeline Company and
American Petrofina Pipe Line Company (incorporated by reference to Exhibit 10.6 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.5
    
    Amendment and Supplement to Pipeline Lease Agreement, dated as of August 31, 2007, by and
between HEP Pipeline Assets, Limited Partnership and Alon USA, LP (incorporated by reference
to Exhibit 10.1 to Form 10-Q, filed by the Company on November 8, 2007).10.6
    
    Contribution Agreement, dated as of January 25, 2005, among Holly Energy Partners, L.P.,
Holly Energy Partners  Operating, L.P., T & R Assets, Inc., Fin-Tex Pipe Line Company,
Alon USA Refining, Inc., Alon Pipeline Assets, LLC, Alon Pipeline Logistics, LLC, Alon USA,
Inc. and Alon USA, LP (incorporated by reference to Exhibit 10.7 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.7
    
    Pipelines and Terminals Agreement, dated as of February 28, 2005, between Alon USA, LP and
Holly Energy Partners, L.P. (incorporated by reference to Exhibit 10.8 to Form S-1, filed by
the Company on May 11, 2005, SEC File No. 333-124797).10.8
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, LP (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
February 5, 2008, SEC File No. 001-32567).10.9
    
    Liquor License Purchase Agreement, dated as of May 12, 2003, between Southwest Convenience
Stores, LLC and SCS Beverage, Inc. (incorporated by reference to Exhibit 10.34 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.10
    
    Premises Lease, dated as of May 12, 2003, between Southwest Convenience Stores, LLC and SCS
Beverage, Inc. (incorporated by reference to Exhibit 10.35 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.11
    
    Amended Revolving Credit Agreement, dated as of January 14, 2004, among Alon USA, LP, the
guarantor companies and financial institutions identified therein and Israel Discount Bank
of New York (incorporated by reference to Exhibit 10.19 to Form S-1, filed by the Company on
May 11, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.12
    
    First Amendment, dated as of February 10, 2005, to the Amended Revolving Credit Agreement,
dated as of January 14, 2004, among Alon USA, LP, the guarantor companies and financial
institutions identified therein and Israel Discount Bank of New York (incorporated by
reference to Exhibit 10.20 to Form S-1, filed by the Company on May 11, 2005, SEC File No.
333-124797).10.13
    
    Second Amendment, dated as of June 16, 2005, to the Amended Revolving Credit Agreement,
dated as of January 14, 2004, among Alon USA, LP, the guarantor companies and financial
institutions identified therein and Israel Discount Bank of New York (incorporated by
reference to Exhibit 10.20.1 to Form S-1/A, filed by the Company on June 17, 2005, SEC File
No. 333-124797).10.14
    
    Amended Revolving Credit Agreement, dated as of February 15, 2006, among Alon USA, LP, the
guarantor companies and financial institutions named therein, Israel Discount Bank of New
York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on February 16, 2006, SEC File No. 001-32567).10.15
    
    Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.2 to Form 8-K, filed by the Company on June 26, 2006, SEC File
No. 001-32567).10.16
    
    First Amendment to Amended Revolving Credit Agreement, dated as of August 4, 2006, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.25 to Form 10-K, filed by the Company on March 15, 2007 SEC File
No. 001-32567).10.17
    
    Waiver, Consent, Partial Release and Second Amendment, dated as of February 28, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, Alon USA, LP, Edgington Oil
Company, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on March 5, 2007, SEC File No.
001-32567).10.18
    
    Third Amendment to Amended Revolving Credit Agreement, dated as of June 29, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc.,
Alon USA, LP, the guarantor companies and financial institutions named therein, Israel
Discount Bank of New York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to
Form 8-K, filed by the Company on July 20, 2007, SEC File No. 001-32567).10.19
    
    Waiver, Consent, Partial Release and Fourth Amendment, dated as of July 2, 2008, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.4 to Form 8-K, filed by the Company on July 10, 2008, SEC File
No. 001-32567).10.20
    
    Credit Agreement, dated as of June 6, 2006, among Southwest Convenience Stores, LLC, the
lenders party thereto and Wachovia Bank, National Association (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on June 7, 2006, SEC File No. 001-32567).10.21
    
    Amended and Restated Credit Agreement, dated as of June 29, 2007, among Southwest
Convenience Stores, LLC, the lenders party thereto and Wachovia Bank, National Association
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on July 2,
2007, SEC File No. 001-32567).10.22
    
    Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc., the lenders party
thereto and Credit Suisse (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by
the Company on June 26, 2006, SEC File No. 001-32567).10.23
    
    Amendment No. 1 to the Credit Agreement, dated as of February 28, 2007, by and among Alon
USA Energy, Inc., the lenders party thereto and Credit Suisse (incorporated by reference to
Exhibit 10.3 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.24
    
    Second Amended and Restated Credit Agreement, dated as of February 28, 2007, among Paramount
Petroleum Corporation, Bank of America, N.A. and certain other guarantor companies and
financial institutions from time to time named therein (incorporated by reference to Exhibit
10.1 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.25
    
    First Amendment to Second Amended and Restated Credit Agreement, dated as of March 30, 2007,
among Paramount Petroleum Corporation, Bank of America, N.A. and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.37 to Form 10-K, filed by the Company on March 11, 2008, SEC File
No. 001-32567).10.26
    
    Term Loan Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., the lenders party thereto and Credit Suisse, as
administrative agent and collateral agent (incorporated by reference to Exhibit 10.2 to Form
8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.27
    
    Loan and Security Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank of America,
N.A., as administrative agent (incorporated by reference to Exhibit 10.3 to Form 8-K, filed
by the Company on July 10, 2008, SEC File No. 001-32567).10.28
    
    First Amendment to Loan and Security Agreement, dated as of December 18, 2008, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto
and Bank of America, N.A.10.29
    
    Credit Agreement, dated as of July 30, 2008, among Alon USA Energy, Inc., the financial
institutions from time to time a party thereto, Israel Discount Bank and Bank Leumi USA
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on August 1,
2008, SEC File No. 001-32567).10.30
    
    Management and Consulting Agreement, dated as of August 1, 2003, among Alon USA, Inc., Alon
Israel Oil Company, Ltd. and Alon USA Energy, Inc. (incorporated by reference to Exhibit
10.21 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.31
    
    Amendment, dated as of June 17, 2005, to the Management and Consulting Agreement, dated as
of August 1, 2003, among Alon USA, Inc., Alon Israel Oil Company, Ltd. and Alon USA Energy,
Inc. (incorporated by reference to Exhibit 10.21.1 to Form S-1/A, filed by the Company on
June 17, 2005, SEC File No. 333-124797).10.32
    
    Registration Rights Agreement, dated as of July 6, 2005, between Alon USA Energy, Inc. and
Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.22 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.33*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Jeff D. Morris and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.23 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.34*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA GP, LLC (incorporated by reference to Exhibit 10.9 to Form 10-Q,
filed by the Company on November 7, 2008, SEC File No. 001-32567).10.35*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Claire A. Hart and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.24 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.36*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Claire A. Hart and Alon USA GP, LLC (incorporated by reference to Exhibit 10.10 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.37*
    
    Executive Employment Agreement, dated as of February 5, 2001, between Joseph A. Concienne,
III and Alon USA GP, Inc., as amended by the Amendment to Executive/Management Employment
Agreement, dated May 1, 2005 (incorporated by reference to Exhibit 10.25 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.38*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Joseph A. Concienne, III and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.11
to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.39*
    
    Amended and Restated Management Employment Agreement, dated as of August 9, 2006, between
Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on August 10, 2006, SEC File No. 001-32567).10.40*
    
    Amendment to Amended and Restated Management Employment Agreement, dated as of November 4,
2008, between Harlin R. Dean and Alon USA GP, LLC. (incorporated by reference to Exhibit
10.12 to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.41*
    
    Management Employment Agreement, dated as of September 1, 2000, between Yosef Israel and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.33 to Form 10-K, filed by the
Company on March 15, 2006, SEC File No. 001-32567).10.42*
    
    Amendment to Executive/Management Employment Agreement, dated as of May 1, 2005 between
Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.34 to Form 10-K,
filed by the Company on March 15, 2006, SEC File No. 001-32567).10.43*
    
    Second Amendment to Executive/Management Employment Agreement, dated as of November 4, 2008,
between Yosef Israel and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.13 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.44*
    
    Executive Employment Agreement, dated as of August 1, 2003, between Shai Even and Alon USA
GP, LLC (incorporated by reference to Exhibit 10.49 to Form 10-K, filed by the Company on
March 15, 2007, SEC File No. 001-32567).10.45*
    
    Amendment to Executive Employment Agreement, dated as of November 4, 2008, between Shai Even
and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.14 to Form 10-Q, filed by the
Company on November 7, 2008, SEC File No. 001-32567).10.46*
    
    Annual Cash Bonus Plan (incorporated by reference to Exhibit 10.27 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.47*
    
    Description of 10% Bonus Plan (incorporated by reference to Exhibit 10.28 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.48*
    
    Description of Annual Bonus Plans (incorporated by reference to Exhibit 10.2 to Form 10-Q,
filed by the Company on June 6,, 2008, SEC File No. 001-32567).10.49*
    
    Change of Control Incentive Bonus Program (incorporated by reference to Exhibit 10.29 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.50*
    
    Description of Director Compensation (incorporated by reference to Exhibit 10.30 to Form
S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.51*
    
    Form of Director Indemnification Agreement (incorporated by reference to Exhibit 10.31 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.52*
    
    Form of Officer Indemnification Agreement (incorporated by reference to Exhibit 10.32 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.53*
    
    Form of Director and Officer Indemnification Agreement (incorporated by reference to Exhibit
10.33 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.54*
    
    Alon Assets, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.36 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.55*
    
    Alon USA Operating, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.37
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.56*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 (incorporated by reference to Exhibit 10.38 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.57 *
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon Assets, Inc. (incorporated by reference to Exhibit 10.15 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.58
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Jeff D.
Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.39 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.59*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 (incorporated by reference to Exhibit 10.40 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.60*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA Operating, Inc. (incorporated by reference to Exhibit 10.16 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.61
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and Jeff
D. Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.41 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.62*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Claire A. Hart, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.42 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.63
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Claire A.
Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.43 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.64*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Claire A. Hart, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.44
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.65
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and
Claire A. Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30,
2002 (incorporated by reference to Exhibit 10.45 to Form S-1/A, filed by the Company on June
17, 2005, SEC File No. 333-124797).10.66*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon Assets, Inc.
and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.46 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).




---



##### 



Exhibit No.
    
    Description of Exhibit10.67
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon Assets, Inc. and Joseph A.
Concienne, III (incorporated by reference to Exhibit 10.47 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.68*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon USA Operating,
Inc. and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.48 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.69
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon USA Operating, Inc. and
Joseph A. Concienne, III (incorporated by reference to Exhibit 10.49 to Form S-1/A, filed by
the Company on June 17, 2005, SEC File No. 333-124797).10.70*
    
    Agreement of Principles of Employment, dated as of July 6, 2005, between David Wiessman and
Alon USA Energy, Inc. (incorporated by reference to Exhibit 10.50 to Form S-1/A, filed by
the Company on July 7, 2005, SEC File No. 333-124797).10.71*
    
    Management Employment Agreement, dated as of October 30, 2008, between Michael Oster and
Alon USA GP,LLC.10.72*
    
    Alon USA Energy, Inc. 2005 Incentive Compensation Plan, as amended on November 7, 2005
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on November 8,
2005, SEC File No. 001-32567).10.73*
    
    Agreement, dated as of July 6, 2005, among Alon USA Energy, Inc., Alon USA, Inc., Alon USA
Capital, Inc., Alon USA Operating, Inc., Alon Assets, Inc., Jeff D. Morris, Claire A. Hart
and Joseph A. Concienne, III (incorporated by reference to Exhibit 10.52 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.74*
    
    Form of Restricted Stock Award Agreement relating to Director Grants pursuant to Section 12
of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on August 5, 2005, SEC File No. 001-32567).10.75*
    
    Form of Restricted Stock Award Agreement relating to Participant Grants pursuant to Section
8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference
to Exhibit 10.1 to Form 8-K, filed by the Company on August 23, 2005, SEC File No.
001-32567).10.76*
    
    Form II of Restricted Stock Award Agreement relating to Participant Grants pursuant to
Section 8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.3 to Form 8-K, filed by the Company on November 8, 2005, SEC File
No. 001-32567).10.77*
    
    Form of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on March 12, 2007, SEC File No.
001-32567).10.78
    
    Purchase and Sale Agreements, dated as of February 13, 2006, between Alon Petroleum Pipe
Line, LP and Sunoco Pipelines, LP, (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on February 13, 2006, SEC File No. 001-32567).10.79
    
    Stock Purchase Agreement, dated as of April 28, 2006, among Alon USA Energy, Inc., The Craig
C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The Jerrel C. Barto and
Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy, III and Mark R. Milano
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on May 2, 2006,
SEC File No. 001-32567).10.80
    
    First Amendment to Stock Purchase Agreement, dated as of June 30, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.1 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).




---



##### 



Exhibit No.
    
    Description of Exhibit10.81
    
    Second Amendment to Stock Purchase Agreement, dated as of July 31, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.2 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.82
    
    Agreement and Plan of Merger, dated as of April 28, 2006, among Alon USA Energy, Inc., Apex
Oil Company, Inc., Edgington Oil Company, and EOC Acquisition, LLC (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on May 2, 2006, SEC File No.
001-32567).10.83
    
    Agreement and Plan of Merger, dated March 2, 2007, by and among Alon USA Energy, Inc., Alon
USA Interests, LLC, ALOSKI, LLC, Skinnys, Inc. and the Davis Shareholders (as defined
therein) (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
March 6, 2007, SEC File No. 001-32567).10.84
    
    Stock Purchase Agreement, dated May 7, 2008, between Valero Refining and Marketing Company
and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.1 to Form
8-K, filed by the Company on May 13, 2008, SEC File No. 001-32567).10.85
    
    First Amendment to Stock Purchase Agreement, dated as of July 3, 2008, by and among Valero
Refining and Marketing Company, Alon Refining Krotz Springs, Inc. and Valero Refining
Company-Louisiana (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on July 10, 2008, SEC File No. 001-32567).10.86
    
    Series A Preferred Stock Purchase Agreement, dated as of July 3, 2008, by and between Alon
Refining Louisiana, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to
Exhibit 10.5 to Form 8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.87
    
    Stockholders Agreement, dated as of July 3, 2008, by and among Alon USA Energy, Inc., Alon
Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.
(incorporated by reference to Exhibit 10.6 to Form 8-K, filed by the Company on July 10,
2008, SEC File No. 001-32567).10.88
    
    Amended and Restated Stockholders Agreement dated as of March 31, 2009, by and among Alon USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.10.89
    
    Offtake Agreement, dated as of July 3, 2008, by and between Valero Marketing and Supply
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.9 to
Form 10-Q, filed by the Company on August 7, 2008, SEC File No. 001-32567).10.90
    
    Earnout Agreement, dated as of July 3, 2008, by and between Valero Refining and Marketing
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.10 to
Form 10-Q, filed by the Company on August 7, 2008, SEC File No. 001-32567).21.1
    
    Subsidiaries of Alon USA Energy, Inc.23.1
    
    Consent of KPMG LLP.31.1
    
    Certifications of Chief Executive Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certifications of Chief Financial Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.32.1
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
§1350, as adopted pursuant to §906 of the Sarbanes-Oxley Act of 2002.
 
 *
    
    Identifies management contracts and compensatory plans or arrangements.
    
    Filed under confidential treatment request.